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Per Table: 1 “strip” of test wells; viral antigen solution (EBV), positive and negative control solutions, anti- IgG peroxidase conjugate (second antibody solution), Phosphate buffered saline (PBS, for washing steps), substrate solution, 4 “unknown” donor serum samples.
Follow all directions carefully. Be particularly careful to avoid cross-contamination of the solutions.
1. Label the first 6 wells of your strip 1-6.
2. Add 50 µl of EBV (viral antigens) to each of the 6 wells using the P200 pipettor.
3. Incubate for 5 minutes at room temperature.
4. Remove the liquid using a transfer pipet. Discard the liquid in the beaker labeled “liquid waste.”
5. Using a transfer pipet, add PBS to each of the 6 wells until almost full (do not allow them to spill over). Be careful not to touch the transfer pipet to the well.
6. Remove the liquid from the well as demonstrated by your instructor (Important: do NOT use the PBS transfer pipet to remove the liquid- this will result in contamination of the PBS with antigen.
7. Add 50 µl of the appropriate test reagent to each well as outlined in the table below. Use a new pipet tip for each solution!
|Well #||Test Reagent||Description|
|1||(-) PBS||Negative control|
|3||DS 1||Donor serum 1|
|4||DS 2||Donor serum 2|
|5||DS 3||Donor serum 3|
|6||DS 4||Donor serum 4|
8. Incubate at 37˚C for 15 minutes.
9. Remove all the liquid from each well with a new pipet tip for each.
10. Wash each well once with PBS. (You can use the same tip for all of the wells provided you don’t contaminate the tip.)
11. Add 50 µl of anti-IgG peroxidase conjugate (secondary antibody) to each of the 6 wells (see above).
12. Incubate at 37˚C for 15 minutes.
13. Remove the liquid from each well.
14. Wash each well twice with PBS.
15. Add 50 µl of the substrate to each of the 6 wells.
16. Incubate at 37˚C for 5 minutes.
17. Remove the test strip from the incubator and examine each well. Development of a color reaction is an indication of a positive result.
Wells may be incubated for a longer period of time if the color reaction does not develop after 5 minutes
Before you begin: make note of the appearance of growth on your agar plate. Record appearance of growth as you have before. More information about the contents of the wells and how the test is set up can be found by watching the videos found at this link: www.biolog.com/videos.php
Per table: one Biolog microplate, 1 swab for picking up bacterial growth, 1 tube of inoculation fluid, 1 reservoir, 1 multichannel pipettor (octapet), pipet tips, and an empty pipet tip box
1. Unwrap your Biolog microplate and label it on the side of the plate with your table number. Place the plate over a white sheet of paper to make the wells more visible.
2. Use a swab to pick up a small amount of bacterial growth from your agar plate (your instructor will guide you as to how much to pick up).
It’s very important not to add too many cells to the tube. It is easier to correct the mistake of not adding enough than it is to correct adding too much, so go slowly!
3. Transfer the cells you have picked up into a tube of inoculating fluid to make a suspension.
4. Mix thoroughly and break up any clumps (vortex gently if needed).
5. Use the turbidimeter (a machine that estimates the concentration of cells in a suspension based on its turbidity) to determine the % transmittance (how much light passes through) for your sample. Ideally this should be 90-98%. Your instructor will assist you with this part.
6. When your sample is at the proper % transmittance, add the contents of the entire tube into a clean reservoir.
7. Secure 8 pipet tips onto the octapet. Make sure all the tips are firmly attached.
8. Use the pipet tips to transfer 100 µl to each of the 98 wells (8 at a time)
It is very important to do this step carefully.
a) Be sure you are pipetting the correct amount of fluid. (If you pipet too much you will run out of your suspension before inoculating all wells).
b) After drawing up the suspension, check the pipet tips—they should all have the same amount and should be free of bubbles. If they do not, release the suspension back into the reservoir and start again.
c) Always start on the left side of the plate (so A1, the negative control, gets inoculated first).
d) Make sure your tips (all 8) are directly over the wells before beginning to release the bacterial suspension from the pipet tip.
e) DO NOT let the tips touch the bottom of the wells. If you do this you will be transferring small amounts of substrate/tetrazolium dye, which could lead to false positive results.
f) After each 2-3 transfers, use the empty pipet tip holder to press the tips back into place (they may become loose after a few uses).
9. Replace the lid on the plate, and incubate your sample at 33˚C.
10. Your plate will be incubated until color development is complete (3-36 hours) and then refrigerated until you can read the results.
11. Discard all contaminated materials (inoculation fluid tube, inoculator, reservoir and pipet tips as instructed. DO NOT put any of these items in the regular garbage.
Identify the basic characteristics of life and outline the theories that attempt to explain the origin of life, as we know it and define it, on the planet Earth.
Identify some basic chemical concepts and apply them to the structure and biological processes that occur in living cells.
Identify cell parts, and demonstrate understanding of their related functions. Identify similarities and differences in the structure of viruses, prokaryotic cells, and eukaryotic cells
Explain the significance of enzymes, coenzymes, and ATP, and to identify the main events, products and significance of the processes of cell respiration, fermentation, and photosynthesis
Understand, explain, and contrast the processes of mitosis, meiosis, and binary fission in terms of their physical differences and their genetic and evolutionary significance. Explain the process of viral replication
Identify the structural parts of DNA and RNA, and understand how DNA directs the activities of a cell through protein synthesis, including some examples of how this process is regulated
Demonstrate understanding of how genes are passed from one generation to the next by completing representative genetic problems and explaining/applying genetic concepts
Demonstrate understanding of the three Domains of Life (Archaea, Bacteria and Eukarya) and viruses. Identify some of the distinguishing characteristics of each domain and the viruses
Learn and apply the laboratory skills associated with the objectives listed above
Explain the basic concepts of biology in written and oral form
Apply the concepts learned to better understand the biological world, and the problems that affect human society
11.1 Punnett square
The Punnett square (Figures 11.1 and 11.2) is a visual representation of Mendelian inheritance and used to predict an outcome of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach. In our first experiment, both parents are homozygous, one carrying two copies of the dominant allele (R), the other two copies of the recessive (r) allele. Each parent can only make gametes that have either the R (purple) or r (yellow) allele. The Punnett square for the parental cross is shown in Figure 11.1
Figure 11.1: Punnett square for homozygous cross.
The squares containing the single letters represent the possible gametes. The squares with two letters represent the zygotes resulting from the combination of the respective gametes. It can be easily seen that all offspring will be heterozygous (Rr) and therefore purple. The Punnett square for the F1 cross is depicted in Figure 11.2
Figure 11.2: Punnett square for heterozygous cross.
During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes.
Describe the stages and results of Meiosis II
- During prophase II, chromsomes condense again, centrosomes that were duplicated during interphase I move away from each other toward opposite poles, and new spindles are formed.
- During prometaphase II, the nuclear envelopes are completely broken down, and each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles.
- During metaphase II, sister chromatids are condensed and aligned at the equator of the cell.
- During anaphase II sister chromatids are pulled apart by the kinetochore microtubules and move toward opposite poles.
- During telophase II and cytokinesis, chromosomes arrive at opposite poles and begin to decondense the two cells divide into four unique haploid cells.
- meiosis II: the second part of the meiotic process the end result is production of four haploid cells from the two haploid cells produced in meiosis I
Meiosis II initiates immediately after cytokinesis, usually before the chromosomes have fully decondensed. In contrast to meiosis I, meiosis II resembles a normal mitosis. In some species, cells enter a brief interphase, or interkinesis, before entering meiosis II. Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in meiosis I go through the events of meiosis II together. During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes. The mechanics of meiosis II is similar to mitosis, except that each dividing cell has only one set of homologous chromosomes.
If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes that were duplicated during interphase I move away from each other toward opposite poles and new spindles are formed.
The nuclear envelopes are completely broken down and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles.
The sister chromatids are maximally condensed and aligned at the equator of the cell.
The sister chromatids are pulled apart by the kinetochore microtubules and move toward opposite poles. Non-kinetochore microtubules elongate the cell.
Meiosis I vs. Meiosis II: The process of chromosome alignment differs between meiosis I and meiosis II. In prometaphase I, microtubules attach to the fused kinetochores of homologous chromosomes, and the homologous chromosomes are arranged at the midpoint of the cell in metaphase I. In anaphase I, the homologous chromosomes are separated. In prometaphase II, microtubules attach to the kinetochores of sister chromatids, and the sister chromatids are arranged at the midpoint of the cells in metaphase II. In anaphase II, the sister chromatids are separated.
Telophase II and Cytokinesis
The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four unique haploid cells. At this point, the newly-formed nuclei are both haploid. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombining of maternal and paternal segments of chromosomes (with their sets of genes) that occurs during crossover.
Complete Stages of Meiosis: An animal cell with a diploid number of four (2n = 4) proceeds through the stages of meiosis to form four haploid daughter cells.
Using genetic data to infer the time of migrations has always been difficult, and the time estimates obtained often come within wide confidence intervals, making these dates unreliable and inferences problematic. Here, we have introduced an approach that takes advantage of dense genome-wide SNP data to improve precision and reduce bias in making inferences about the timing of human migrations. By using an admixed population one can capitalize on the property of the genome to recombine each generation, producing chromosomes that are a mixture of the parental genetic material. The structure of an admixed genome contains temporal information about an admixture event, as a greater number and narrower width of ancestry blocks indicates more recombination events, and hence greater time depth.
Simulations indicate that the WT coefficients can be used to obtain accurate estimates of the time of admixture from suitable genome-wide SNP data. We therefore applied the method to three datasets, consisting of about 650,000 SNPs, to estimate the amount and time of admixture for three human populations: African-Americans, Polynesians, and Fijians. In addition, we analyzed and dated admixture in five HGDP populations of African and Middle-Eastern origin. At first glance, it may appear that the simulated and empirical data differ in that the simulations used fully-differentiated populations, which is not the case for the empirical data. However, as explained in more detail in the Results and Discussion (Basic Setup section), the number of SNPs is adjusted in the StepPCO sliding windows until the ancestral populations can be statistically-differentiated, just as with the simulated data.
For African-Americans, we estimate an average of 19% European ancestry, with a wide range of less than 5% to more than 40% European ancestry across individuals. Both the average and the observation of a wide range of individual admixture estimates are in keeping with previous studies [10, 17, 36, 37]. The estimated time of admixture is about 180 years ago (95% CI: 120-240 years ago), which is probably an underestimate since admixture in the African-American population is ongoing (implying that new ancestry blocks are being continuously introduced by new recombination events, which potentially removes older block structure by replacing narrower ancestry blocks with new, wider blocks).
We tested the performance of the method on Fijians and Polynesians, as both populations are of admixed Asian and Melanesian ancestry . Previous demographic analyses of the genome-wide SNP data used in this study strongly support both an admixed Asian/Melanesian ancestry for Fijians and Polynesians as well as subsequent additional gene flow from Melanesia into Fiji, but not Polynesia . Based on this previously established scenario, we estimated an average of about 25% (from 18 to 28%) Melanesian ancestry in Polynesians, in good agreement with previous estimates based on the same  or other [6, 38–40] data. The estimated time of admixture is about 90 generations ago, or 2,700 years (95% CI: 2,300-3,900 years), in good agreement with a previous estimate of about 3,000 years ago based on an ABC simulation approach for the same data . For Fiji, the estimated amount of Melanesian ancestry was about 40%, and the time for this admixture is estimated to have occurred about 37 generations ago, or 1,100 years (95% CI: 870-1170 years). An ABC-simulation based approach for the same data gave an estimated date of 62 generations for this admixture in Fijians, about twice as long ago as our estimate. We speculate that, as in the case of the African-Americans, the estimate based on WT coefficients may be biased toward more recent dates if the gene flow to Fiji occurred over a period of time, as more recent gene flow replaces older, narrower ancestry blocks with newer, wider ancestry blocks. Individual Melanesian ancestry estimates are much wider for Fiji (from 22 to 63%) than for Polynesia (from 18 to 28%), which may indeed indicate a longer period of gene flow into Fiji.
Our results for the Mozabite, Mandenka, Bedouin, Druze and Palestinian populations are similar to those for HAPMIX for inferring local ancestry, and in addition our method seems to perform better with respect to more ancient admixture events (as also shown with simulated data: Figure 4). In particular, we dated the admixture event in the Mozabites and the Druze to 131 and 90 generations ago respectively, 30 generations more than the corresponding estimates obtained with HAPMIX . HAPMIX estimation of the time since admixture is based on the number of calculated ancestry transitions (that is, the number of breakpoints) both our simulations and previous simulations  indicate that infinite size populations the number of breakpoints does not increase with time according to expectations (see Equation 1 above), but rather stabilizes, leading to underestimates in admixture dates (Figure 2b). Furthermore, because human populations are closely related and not very well differentiated, direct estimation of the number of breakpoints and block width as a measure of time since admixture for human genetic data is problematic for two reasons. Firstly, to have enough power to reliably assign chromosomal segments to an ancestral population, it is necessary to use relatively large genomic windows, which correspondingly reduces detection of closely-spaced breakpoints. And secondly, for every location in the genome that potentially carries a breakpoint, a formal decision has to be made as to whether to consider it a true breakpoint or not. This transformation of the 'raw' signal into a discrete signal potentially leads to either some not well-defined breakpoints being overlooked, or conversely random effects becoming inflated and falsely considered as a true signal. These errors, however small, will accumulate over the many measurements taken. Conversely, the spectral analysis approach implemented here does not require any data transformation and is applied to the 'raw' signal directly. This has the advantage of preserving the statistical nature of the signal until the final averaging step, and thus does not involve detection of exact location (and presence) of breakpoints, where inevitably large errors in estimation could occur. Although we followed Price et al. 2009 in using African and European parental groups for the admixed Mozabite, Mandenka, Bedouin, Druze and Palestinian groups from the CEPH-HGDP, in fact previous studies have shown that the Druze, Bedouin and Palestinian populations are admixed primarily along a European-Central Asian axis, with little African admixture, and the Mandenka exhibit very little European admixture [18, 41]. Here, we report dates for the presumptive European gene flow, to compare our results to the previous study , but it is important to keep in mind that our method (like all admixture methods) requires the use of pre-defined parental groups. Incorrect identification of the ancestral groups contributing to an admixed group will obviously lead to erroneous conclusions, hence careful attention must be paid when identifying parental groups. This is especially true for groups that are suggested to have experienced admixture a long time ago, and hence had more time to experience genetic drift (which is always expected to act in a direction orthogonal to the axis of admixture). In such cases, it is difficult to distinguish between an admixed population that has been subject to genetic drift, and a population that has experienced admixture along a different axis of variation.
Theoretically, there are no limitations as to how far back in time one can get good estimates of admixture time with WT coefficients. The performance of the method is influenced by two factors: the density of SNPs analyzed and the degree of differentiation between the two parental populations. Increasing SNP density would allow the estimated time horizon for detecting admixture to be moved further back. We therefore expect that full sequence data will increase the sensitivity and resolution of our method. The analysis presented here was based on about 650,000 markers the current estimates for the number of SNPs in the human genome is around 15 million SNPs . Full sequence data will thus provide a twentyfold increase in SNP density, and thereby allow for a twentyfold reduction in the size of the sliding window. Thus, assuming that the newly added SNPs are no less informative for population differentiation than the SNPs on the Affymetrix arrays, we expect that analysis of full sequence data should offer at least a twentyfold improvement in the potential time depth for admixture estimates for human populations. However, given that there is relatively little genetic differentiation between human populations, to distinguish among parental populations requires relatively large segments of the genome, and this also poses a restriction on the time depth of the method. The more closely-related the parental populations, the larger the window size needed to span a sufficient number of informative SNPs. Obviously, this limitation will persist regardless of the type of molecular data considered. However, because of the strong ascertainment bias associated with the SNPs genotyped on the arrays, we expect that SNP-data generated using the array technology necessarily underestimates the variation that exists between human populations, and recent studies suggest that this underestimation could be considerable . Moreover, the method introduced here can be used with any species for which suitable genome-wide data exist, and the larger the genetic difference among the parental populations, the less genome-wide data needed for accurate admixture estimates.
An additional advantage of the StepPCO method is that it provides an estimate of the admixture proportions for each individual within an admixed population. Individual-level estimates of admixture obtained here via StepPCO for African-Americans, Polynesians, and Fijians were quite similar to those obtained via the maximum-likelihood based approach frappe , indicating that StepPCO gives reliable results. Furthermore, the StepPCO method also provides information about the distribution of admixture along each chromosome. As such, this approach is also promising for disease gene mapping (in recently admixed populations), and for studying local selection. According to neutral expectations the admixture level should be constant along the genome, but a locus favored by positive selection in the admixed population should appear to have greater admixture proportions than would be expected from the genome-wide average. We are currently investigating the utility of this approach for identifying candidate genes subject to local selection.
In conclusion, we have shown that wavelet transformation is a useful and novel means of dating admixture events from genome-wide data. Other potential extensions of the methodology introduced here include admixture scenarios involving more than two parental populations, and implementing spectral analysis of the raw genomic signal directly, rather than from the StepPCO signal. There is potentially much more to be learned from surfing the wavelets of the genome.
The Lakehead Advantage
Our location in the Boreal Forest makes Lakehead University the ideal institution to study Biology. We host intensive local field trips and field schools for our undergraduate students, making the most of the environment and wildlife available to us. While many other universities have to travel to get this experience, we can host our field trips within the 3 hours allotted for a class or a lab.
As a Biology student you will have access to the Lakehead University Instrumentation Lab (LUIL) and learn to operate the tools and equipment to conduct your own research and generate data yourself. Unlike other universities, you can utilize the lab as opposed to passing your samples on to a technician. This practical knowledge gives you an advantage when applying to graduate or professional school or a science-based job.
Our relatively small class sizes provide exceptional networking opportunities with faculty members. This is especially helpful if you are considering pursuing an Honours Thesis or research project as you will require an academic advisor. Our faculty is well connected within the community and the industry, making such relationships very conducive to summer job opportunities.
Conducting Lab Using Probes and Computer/Calculator
Tip: "My AP Biology class just finished the Aquatic Productivity Lab using a long-term computer interfacing setup. We used pH probes to follow the carbonic acid (CO2) levels over time (90 hours) in four miniature aquatic ecosystems. The samples were taken from a small pond and included some visible algae and other 'critters.' The bottles were placed under a light stand with a timer set for 12 hours light/12 hours dark.
"Our dissolved oxygen readings came out as follows:
After 90 hours (alternating 12 hours light/12 hours dark):
1 Screen-5.6 ppm
2 Screens-4.0 ppm
4 Screens-1.6 ppm
"A bottle kept in continuous darkness had 1.4 ppm. This experiment is one I highly recommend for computer interfacing. The changes over time (90 hours) in the various systems with the changing day/night cycles are something that the 'regular' method of doing this lab misses entirely."
—Jeff Smith, Indiana Academy, Muncie, Indiana. 4/26/99
12.2.2021 M.Sc. Chandan Thapa (Faculty of Mathematics and Science, Cell and Molecular Biology) ONLINE EVENT
Cancer is a result of the uncontrolled growth of cells, which is caused by the deregulation of multiple cellular pathways that are involved in normal growth control. Numerous studies highlight the importance of the enzyme complex called Protein phosphatase 2A (PP2A) in the inhibition of the transformation of normal human cells into cancerous cells.
The PP2A activity is inhibited by different proteins such as ARPP-16, ARPP-19, and ENSA. These proteins have been shown to play role in several cancer types such as hepatocellular carcinoma, human glioma, acute myeloid carcinoma, gastric cancer, breast cancer, and papillary thyroid cancers. Therapeutically, it is tempting to reactivate PP2A by inhibiting the interaction of PP2A and PP2A inhibitor proteins by using small molecules. For that, it is essential to understand the molecular and structural mechanism of PP2A inhibition by inhibitor proteins such as ARPP-16, ARPP-19, and ENSA.
Understanding the inhibitory mechanism
The ultimate aim of this study was to reveal the mechanism of how ARPP-16, ARPP-19, and ENSA proteins inhibit PP2A function. Understanding the inhibitory mechanism is crucial to develop small molecule modulators that can treat cancer types linked to these proteins. Considering that, we first integrated the modern structural biology methods such as NMR spectroscopy and small-angle X-ray scattering methods to investigate so far unknown structural properties of the PP2A inhibitor proteins ARPP-19, ARPP-16, and ENSA.
The results show that the ARPP and ENSA proteins lack the defined three-dimensional structure being intrinsically disordered proteins but have propensities to form transient secondary structures. Both ARPPs and ENSA have three short transient helical regions and these preformed structures can act as recognition elements during interaction with their partner. Intrinsic disorder proteins are multifaceted and manifest themselves in various forms that allow them to exert different functions in a different cellular context.
We used microscale thermophoresis and NMR spectroscopy techniques to understand the interaction mechanism between the PP2A and ARPPs/ENSA. The interaction studies showed that ARPP and ENSA proteins interact differently with different PP2A subunits. ARPP/ENSA proteins bind to PP2A A-subunit with modest affinity, whereas the interaction to the regulatory B-subunit is weak and transient.
Our studies also revealed that ARPPs and ENSA utilize different regions in their interaction with PP2A scaffolding A-subunit ARPPs bind to A-subunit via a linear motif comprising the second transient α-helical region, whereas ENSA binds to PP2A A-subunit using extended binding region that comprise all three transient α-helical regions.
Accordingly, both ARPPs and ENSA seem to utilize a two-step mechanism in the binding with PP2A. In the first step, ARPPs/ENSA binds to the target site on the A-subunit of PP2A. In the next step, the interaction of ARPPs/ENSA to the B-subunit of PP2A is guided by the local interaction with the target site at A-subunit. Although our results do not give a complete molecular and structural level explanation for the ARPP mediated PP2A inhibition, our results provide a good starting point for future studies and the development of therapeutics that block ARPPs/ENSA – PP2A interaction and reactive PP2A.
The research is published in the JYU Dissertations series, number 346, University of Jyväskylä, Jyväskylä, 2021. ISBN 978-951-39-8486-1 (PDF), URN:ISBN:978-951-39-8486-1, ISSN 2489-9003
Link to the publication: http://urn.fi/URN:ISBN:978-951-39-8486-1
M.Sc. Chandan Thapa defends his doctoral dissertation in Cell and Molecular Biology "Structural insight of PP2A inhibitor proteins and their interaction with PP2A A- and B56-subunit" at the University of Jyväskylä on Friday 12th of February 2021 starting at noon. Opponent Professor is Mark S. Johnson (Åbo Akademi) and Custos is Professor Perttu Permi (University of Jyväskylä). The doctoral dissertation is held in English.
The audience can follow the dissertation online.
Link to the online event: https://r.jyu.fi/dissertation-thapa-120221
Phone number to which the audience can present possible additional questions at the end of the event (to the custos): +358 40 805 4288
"Biology" derives from the Ancient Greek words of βίος romanized bíos meaning "life" and -λογία romanized logía (-logy) meaning "branch of study" or "to speak".   Those combined make the Greek word βιολογία romanized biología meaning biology. Despite this, the term βιολογία as a whole didn't exist in Ancient Greek. The first to borrow it was the English and French (biologie). Historically there was another term for "biology" in English, lifelore it is rarely used today.
The Latin-language form of the term first appeared in 1736 when Swedish scientist Carl Linnaeus (Carl von Linné) used biologi in his Bibliotheca Botanica. It was used again in 1766 in a work entitled Philosophiae naturalis sive physicae: tomus III, continens geologian, biologian, phytologian generalis, by Michael Christoph Hanov, a disciple of Christian Wolff. The first German use, Biologie, was in a 1771 translation of Linnaeus' work. In 1797, Theodor Georg August Roose used the term in the preface of a book, Grundzüge der Lehre van der Lebenskraft. Karl Friedrich Burdach used the term in 1800 in a more restricted sense of the study of human beings from a morphological, physiological and psychological perspective (Propädeutik zum Studien der gesammten Heilkunst). The term came into its modern usage with the six-volume treatise Biologie, oder Philosophie der lebenden Natur (1802–22) by Gottfried Reinhold Treviranus, who announced: 
The objects of our research will be the different forms and manifestations of life, the conditions and laws under which these phenomena occur, and the causes through which they have been affected. The science that concerns itself with these objects we will indicate by the name biology [Biologie] or the doctrine of life [Lebenslehre].
The earliest of roots of science, which included medicine, can be traced to ancient Egypt and Mesopotamia in around 3000 to 1200 BCE.   Their contributions later entered and shaped Greek natural philosophy of classical antiquity.     Ancient Greek philosophers such as Aristotle (384–322 BCE) contributed extensively to the development of biological knowledge. His works such as History of Animals were especially important because they revealed his naturalist leanings, and later more empirical works that focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus, wrote a series of books on botany that survived as the most important contribution of antiquity to the plant sciences, even into the Middle Ages. 
Scholars of the medieval Islamic world who wrote on biology included al-Jahiz (781–869), Al-Dīnawarī (828–896), who wrote on botany,  and Rhazes (865–925) who wrote on anatomy and physiology. Medicine was especially well studied by Islamic scholars working in Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in upholding a fixed hierarchy of life.
Biology began to quickly develop and grow with Anton van Leeuwenhoek's dramatic improvement of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in entomology and helped to develop the basic techniques of microscopic dissection and staining. 
Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell. Then, in 1838, Schleiden and Schwann began promoting the now universal ideas that (1) the basic unit of organisms is the cell and (2) that individual cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most biologists accepted all three tenets of what came to be known as cell theory.  
Meanwhile, taxonomy and classification became the focus of natural historians. Carl Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever since), and in the 1750s introduced scientific names for all his species.  Georges-Louis Leclerc, Comte de Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility of common descent. Although he was opposed to evolution, Buffon is a key figure in the history of evolutionary thought his work influenced the evolutionary theories of both Lamarck and Darwin. 
Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck, who was the first to present a coherent theory of evolution.  He posited that evolution was the result of environmental stress on properties of animals, meaning that the more frequently and rigorously an organ was used, the more complex and efficient it would become, thus adapting the animal to its environment. Lamarck believed that these acquired traits could then be passed on to the animal's offspring, who would further develop and perfect them.  However, it was the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the uniformitarian geology of Lyell, Malthus's writings on population growth, and his own morphological expertise and extensive natural observations, who forged a more successful evolutionary theory based on natural selection similar reasoning and evidence led Alfred Russel Wallace to independently reach the same conclusions.   Darwin's theory of evolution by natural selection quickly spread through the scientific community and soon became a central axiom of the rapidly developing science of biology.
The basis for modern genetics began with the work of Gregor Mendel, who presented his paper, "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), in 1865,  which outlined the principles of biological inheritance, serving as the basis for modern genetics.  However, the significance of his work was not realized until the early 20th century when evolution became a unified theory as the modern synthesis reconciled Darwinian evolution with classical genetics.  In the 1940s and early 1950s, a series of experiments by Alfred Hershey and Martha Chase pointed to DNA as the component of chromosomes that held the trait-carrying units that had become known as genes. A focus on new kinds of model organisms such as viruses and bacteria, along with the discovery of the double-helical structure of DNA by James Watson and Francis Crick in 1953, marked the transition to the era of molecular genetics. From the 1950s to the present times, biology has been vastly extended in the molecular domain. The genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the goal of mapping the general human genome. This project was essentially completed in 2003,  with further analysis still being published. The Human Genome Project was the first step in a globalized effort to incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and the bodies of other organisms.
Atoms and molecules
All living organisms are made up of matter and all matter is made up of elements.  Oxygen, carbon, hydrogen, and nitrogen are the four elements that account for 96% of all living organisms, with calcium, phosphorus, sulfur, sodium, chlorine, and magnesium accounting for the remaining 3.7%.  Different elements can combine to form compounds such as water, which is fundamental to life.  Life on Earth began from water and remained there for about three billions years prior to migrating onto land.  Matter can exist in different states as a solid, liquid, or gas.
The smallest unit of an element is an atom, which is composed of a nucleus and one or more electrons bound to the nucleus. The nucleus is made of one or more protons and a number of neutrons. Individual atoms can be held together by chemical bonds to form molecules and ionic compounds.  Common types of chemical bonds include ionic bonds, covalent bonds, and hydrogen bonds. Ionic bonding involves the electrostatic attraction between oppositely charged ions, or between two atoms with sharply different electronegativities,  and is the primary interaction occurring in ionic compounds. Ions are atoms (or groups of atoms) with an electrostatic charge. Atoms that gain electrons make negatively charged ions (called anions) whereas those that lose electrons make positively charged ions (called cations).
Unlike ionic bonds, a covalent bond involves the sharing of electron pairs between atoms. These electron pairs and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. 
A hydrogen bond is primarily an electrostatic force of attraction between a hydrogen atom which is covalently bound to a more electronegative atom or group such as oxygen. A ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them. When more molecules are present, as is the case with liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule.
With the exception of water, nearly all the molecules that make up each living organism contain carbon.   Carbon can form very long chains of interconnecting carbon–carbon bonds, which are strong and stable. The simplest form of an organic molecule is the hydrocarbon, which is a large family of organic compounds that are composed of hydrogen atoms bonded to a chain of carbon atoms. A hydrocarbon backbone can be substituted by other atoms. When combined with other elements such as oxygen, hydrogen, phosphorus, and sulfur, carbon can form many groups of important biological compounds such as sugars, fats, amino acids, and nucleotides.
Molecules such as sugars, amino acids, and nucleotides can act as single repeating units called monomers to form chain-like molecules called polymers via a chemical process called condensation.  For example, amino acids can form polypeptides whereas nucleotides can form strands of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Polymers make up three of the four macromolecules (polysaccharides, lipids, proteins, and nucleic acids) that are found in all living organisms. Each macromolecule plays a specialized role within any given cell. Some polysaccharides, for instance, can function as storage material that can be hydrolyzed to provide cells with sugar. Lipids are the only class of macromolecules that are not made up of polymers and the most biologically important lipids are fats, phospholipids, and steroids.  Proteins are the most diverse of the macromolecules, which include enzymes, transport proteins, large signaling molecules, antibodies, and structural proteins. Finally, nucleic acids store, transmit, and express hereditary information. 
Cell theory states that cells are the fundamental units of life, that all living things are composed of one or more cells, and that all cells arise from preexisting cells through cell division.  Most cells are very small, with diameters ranging from 1 to 100 micrometers and are therefore only visible under a light or electron microscope.  There are generally two types of cells: eukaryotic cells, which contain a nucleus, and prokaryotic cells, which do not. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be single-celled or multicellular. In multicellular organisms, every cell in the organism's body is derived ultimately from a single cell in a fertilized egg.
Every cell is enclosed within a cell membrane that separates its cytoplasm from the extracellular space.  A cell membrane consists of a lipid bilayer, including cholesterols that sit between phospholipids to maintain their fluidity at various temperatures. Cell membranes are semipermeable, allowing small molecules such as oxygen, carbon dioxide, and water to pass through while restricting the movement of larger molecules and charged particles such as ions.  Cell membranes also contains membrane proteins, including integral membrane proteins that go across the membrane serving as membrane transporters, and peripheral proteins that loosely attach to the outer side of the cell membrane, acting as enzymes shaping the cell.  Cell membranes are involved in various cellular processes such as cell adhesion, storing electrical energy, and cell signalling and serve as the attachment surface for several extracellular structures such as a cell wall, glycocalyx, and cytoskeleton.
Within the cytoplasm of a cell, there are many biomolecules such as proteins and nucleic acids.  In addition to biomolecules, eukaryotic cells have specialized structures called organelles that have their own lipid bilayers or are spatially units. These organelles include the cell nucleus, which contains a cell's genetic information, or mitochondria, which generates adenosine triphosphate (ATP) to power cellular processes. Other organelles such as endoplasmic reticulum and Golgi apparatus play a role in the synthesis and packaging of proteins, respectively. Biomolecules such as proteins can be engulfed by lysosomes, another specialized organelle. Plant cells have additional organelles that distinguish them from animal cells such as a cell wall, chloroplasts, and vacuole.
All cells require energy to sustain cellular processes. Energy is the capacity to do work, which, in thermodynamics, can be calculated using Gibbs free energy. According to the first law of thermodynamics, energy is conserved, i.e., cannot be created or destroyed. Hence, chemical reactions in a cell do not create new energy but are involved instead in the transformation and transfer of energy.  Nevertheless, all energy transfers lead to some loss of usable energy, which increases entropy (or state of disorder) as stated by the second law of thermodynamics. As a result, living organisms such as cells require continuous input of energy to maintain a low state of entropy. In cells, energy can be transferred as electrons during redox (reduction–oxidation) reactions, stored in covalent bonds, and generated by the movement of ions (e.g., hydrogen, sodium, potassium) across a membrane.
Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration) or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly without being consumed by it – by reducing the amount of activation energy needed to convert reactants into products. Enzymes also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
Cellular respiration is a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products.  The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy because weak high-energy bonds, in particular in molecular oxygen,  are replaced by stronger bonds in the products. Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. The overall reaction occurs in a series of biochemical steps, some of which are redox reactions. Although cellular respiration is technically a combustion reaction, it clearly does not resemble one when it occurs in a living cell because of the slow, controlled release of energy from the series of reactions.
Sugar in the form of glucose is the main nutrient used by animal and plant cells in respiration. Cellular respiration involving oxygen is called aerobic respiration, which has four stages: glycolysis, citric acid cycle (or Krebs cycle), electron transport chain, and oxidative phosphorylation.  Glycolysis is a metabolic process that occurs in the cytoplasm whereby glucose is converted into two pyruvates, with two net molecules of ATP being produced at the same time.  Each pyruvate is then oxidized into acetyl-CoA by the pyruvate dehydrogenase complex, which also generates NADH and carbon dioxide. Acetyl-Coa enters the citric acid cycle, which takes places inside the mitochondrial matrix. At the end of the cycle, the total yield from 1 glucose (or 2 pyruvates) is 6 NADH, 2 FADH2, and 2 ATP molecules. Finally, the next stage is oxidative phosphorylation, which in eukaryotes, occurs in the mitochondrial cristae. Oxidative phosphorylation comprises the electron transport chain, which is a series of four protein complexes that transfer electrons from one complex to another, thereby releasing energy from NADH and FADH2 that is coupled to the pumping of protons (hydrogen ions) across the inner mitochondrial membrane (chemiosmosis), which generates a proton motive force.  Energy from the proton motive force drives the enzyme ATP synthase to synthesize more ATPs by phosphorylating ADPs. The transfer of electrons terminates with molecular oxygen being the final electron acceptor.
If oxygen were not present, pyruvate would not be metabolized by cellular respiration but undergoes a process of fermentation. The pyruvate is not transported into the mitochondrion but remains in the cytoplasm, where it is converted to waste products that may be removed from the cell. This serves the purpose of oxidizing the electron carriers so that they can perform glycolysis again and removing the excess pyruvate. Fermentation oxidizes NADH to NAD + so it can be re-used in glycolysis. In the absence of oxygen, fermentation prevents the buildup of NADH in the cytoplasm and provides NAD + for glycolysis. This waste product varies depending on the organism. In skeletal muscles, the waste product is lactic acid. This type of fermentation is called lactic acid fermentation. In strenuous exercise, when energy demands exceed energy supply, the respiratory chain cannot process all of the hydrogen atoms joined by NADH. During anaerobic glycolysis, NAD + regenerates when pairs of hydrogen combine with pyruvate to form lactate. Lactate formation is catalyzed by lactate dehydrogenase in a reversible reaction. Lactate can also be used as an indirect precursor for liver glycogen. During recovery, when oxygen becomes available, NAD + attaches to hydrogen from lactate to form ATP. In yeast, the waste products are ethanol and carbon dioxide. This type of fermentation is known as alcoholic or ethanol fermentation. The ATP generated in this process is made by substrate-level phosphorylation, which does not require oxygen.
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organism's metabolic activities via cellular respiration. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water.    In most cases, oxygen is also released as a waste product. Most plants, algae, and cyanobacteria perform photosynthesis, which is largely responsible for producing and maintaining the oxygen content of the Earth's atmosphere, and supplies most of the energy necessary for life on Earth. 
Photosynthesis has four stages: Light absorption, electron transport, ATP synthesis, and carbon fixation.  Light absorption is the initial step of photosynthesis whereby light energy is absorbed by chlorophyll pigments attached to proteins in the thylakoid membranes. The absorbed light energy is used to remove electrons from a donor (water) to a primary electron acceptor, a quinone designated as Q. In the second stage, electrons move from the quinone primary electron acceptor through a series of electron carriers until they reach a final electron acceptor, which is usually the oxidized form of NADP + , which is reduced to NADPH, a process that takes place in a protein complex called photosystem I (PSI). The transport of electrons is coupled to the movement of protons (or hydrogen) from the stroma to the thylakoid membrane, which forms a pH gradient across the membrane as hydrogen becomes more concentrated in the lumen than in the stroma. This is analogous to the proton-motive force generated across the inner mitochondrial membrane in aerobic respiration. 
During the third stage of photosynthesis, the movement of protons down their concentration gradients from the thylakoid lumen to the stroma through the ATP synthase is coupled to the synthesis of ATP by that same ATP synthase.  The NADPH and ATPs generated by the light-dependent reactions in the second and third stages, respectively, provide the energy and electrons to drive the synthesis of glucose by fixing atmospheric carbon dioxide into existing organic carbon compounds, such as ribulose bisphosphate (RuBP) in a sequence of light-independent (or dark) reactions called the Calvin cycle. 
Cell communication (or signaling) is the ability of cells to receive, process, and transmit signals with its environment and with itself.   Signals can be non-chemical such as light, electrical impulses, and heat, or chemical signals (or ligands) that interact with receptors, which can be found embedded in the cell membrane of another cell or located deep inside a cell.   There are generally four types of chemical signals: autocrine, paracrine, juxtacrine, and hormones.  In autocrine signaling, the ligand affects the same cell that releases it. Tumor cells, for example, can reproduce uncontrollably because they release signals that initiate their own self-division. In paracrine signaling, the ligand diffuses to nearby cells and affect them. For example, brain cells called neurons release ligands called neurotransmitters that diffuse across a synaptic cleft to bind with a receptor on an adjacent cell such as another neuron or muscle cell. In juxtacrine signaling, there is direct contact between the signaling and responding cells. Finally, hormones are ligands that travel through the circulatory systems of animals or vascular systems of plants to reach their target cells. Once a ligand binds with a receptor, it can influence the behavior of another cell, depending on the type of receptor. For instance, neurotransmitters that bind with an inotropic receptor can alter the excitability of a target cell. Other types of receptors include protein kinase receptors (e.g., receptor for the hormone insulin) and G protein-coupled receptors. Activation of G protein-coupled receptors can initiate second messenger cascades. The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events is called signal transduction
The cell cycle is a series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA and some of its organelles, and the subsequent partitioning of its cytoplasm into two daughter cells in a process called cell division.  In eukaryotes (i.e., animal, plant, fungal, and protist cells), there are two distinct types of cell division: mitosis and meiosis.  Mitosis is part of the cell cycle, in which replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA is replicated) and is often followed by telophase and cytokinesis which divides the cytoplasm, organelles and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define the mitotic phase of an animal cell cycle—the division of the mother cell into two genetically identical daughter cells.  The cell cycle is a vital process by which a single-celled fertilized egg develops into a mature organism, as well as the process by which hair, skin, blood cells, and some internal organs are renewed. After cell division, each of the daughter cells begin the interphase of a new cycle. In contrast to mitosis, meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions.  Homologous chromosomes are separated in the first division (meiosis I), and sister chromatids are separated in the second division (meiosis II). Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor.
Prokaryotes (i.e., archaea and bacteria) can also undergo cell division (or binary fission). Unlike the processes of mitosis and meiosis in eukaryotes, binary fission takes in prokaryotes takes place without the formation of a spindle apparatus on the cell. Before binary fission, DNA in the bacterium is tightly coiled. After it has uncoiled and duplicated, it is pulled to the separate poles of the bacterium as it increases the size to prepare for splitting. Growth of a new cell wall begins to separate the bacterium (triggered by FtsZ polymerization and "Z-ring" formation)  The new cell wall (septum) fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids.
Genetics is the scientific study of inheritance.    Mendelian inheritance, specifically, is the process by which genes and traits are passed on from parents to offspring.  It was formulated by Gregor Mendel, based on his work with pea plants in the mid-nineteenth century. Mendel established several principles of inheritance. The first is that genetic characteristics, which are now called alleles, are discrete and have alternate forms (e.g., purple vs. white or tall vs. dwarf), each inherited from one of two parents. Based on his law of dominance and uniformity, which states that some alleles are dominant while others are recessive an organism with at least one dominant allele will display the phenotype of that dominant allele.  Exceptions to this rule include penetrance and expressivity.  Mendel noted that during gamete formation, the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene, which is stated by his law of segregation. Heterozygotic individuals produce gametes with an equal frequency of two alleles. Finally, Mendel formulated the law of independent assortment, which states that genes of different traits can segregate independently during the formation of gametes, i.e., genes are unlinked. An exception to this rule would include traits that are sex-linked. Test crosses can be performed to experimentally determine the underlying genotype of an organism with a dominant phenotype.  A Punnett square can be used to predict the results of a test cross. The chromosome theory of inheritance, which states that genes are found on chromosomes, was supported by Thomas Morgans's experiments with fruit flies, which established the sex linkage between eye color and sex in these insects.  In humans and other mammals (e.g., dogs), it is not feasible or practical to conduct test cross experiments. Instead, pedigrees, which are genetic representations of family trees,  are used instead to trace the inheritance of a specific trait or disease through multiple generations. 
Deoxyribonucleic acid (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic hereditary information. The two DNA strands are known as polynucleotides as they are composed of monomers called nucleotides.   Each nucleotide is composed of one of four nitrogenous bases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. It is the sequence of these four bases along the backbone that encodes genetic information. Bases of the two polynucleotide strands are bound together by hydrogen bonds, according to base pairing rules (A with T and C with G), to make double-stranded DNA. The bases are divided into two groups: pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine whereas the purines are adenine and guanine. The two strands of DNA run in opposite directions to each other and are thus antiparallel. DNA is replicated once the two strands separate.
A gene is a unit of heredity that corresponds to a region of DNA that influences the form or function of an organism in specific ways. DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell's genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts.  In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid.  The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.  Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism.
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The process is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958.    Gene expression is the most fundamental level at which a genotype gives rise to a phenotype, i.e., observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the synthesis of proteins that control an organism's structure and development, or that act as enzymes catalyzing specific metabolic pathways. A large part of DNA (e.g., >98% in humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. Messenger RNA (mRNA) strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U).  Under the genetic code, these mRNA strands specify the sequence of amino acids within proteins in a process called translation, which occurs in ribosomes. This process is used by all life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. Gene products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA.   All steps in the gene expression process can be regulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Regulation of gene expression gives control over the timing, location, and amount of a given gene product (protein or ncRNA) present in a cell and can have a profound effect on cellular structure and function.
A genome is an organism's complete set of DNA, including all of its genes.  Sequencing and analysis of genomes can be done using high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.    Many genes encode more than one protein, with posttranslational modifications increasing the diversity of proteins within a cell. A cell's proteome is its entire set of proteins expressed by its genome.  The genomes of prokaryotes are small, compact, and diverse. In contrast, the genomes of eukaryotes are larger and more complex such as having more regulatory sequences and much of its genome are made up of non-coding DNA sequences for functional RNA (rRNA, tRNA, and mRNA) or regulatory sequences. The genomes of various model organisms such as arabidopsis, fruit fly, mice, nematodes, and yeast have been sequenced. The sequencing of the entire human genome has yielded practical applications such as DNA fingerprinting, which can be used for paternity testing and forensics. In medicine, sequencing of the entire human genome has allowed for the identification mutations that cause tumors as well as genes that cause a specific genetic disorder. 
Biotechnology is the use of cells or living organisms to develop products for humans.  It includes tools such as recombinant DNA, which are DNA molecules formed by laboratory methods of genetic recombination such as molecular cloning, which bring together genetic material from multiple sources, creating sequences that would otherwise not be found in a genome. Other tools include the use of genomic libraries, DNA microarrays, expression vectors, synthetic genomics, and CRISPR gene editing.   Many of these tools have wide applications such as creating medically useful proteins, or improving plant cultivation and animal husbandry.  Human insulin, for example, was the first medicine to be made using recombinant DNA technology. Other approaches such as pharming can produce large quantities of medically useful products through the use of genetically modified organisms. 
Genes, development, and evolution
Development is the process by which a multicellular organism (plant or animal) goes through a series of a changes, starting from a single cell, and taking on various forms that are characteristic of its life cycle.  There are four key processes that underlie development: Determination, differentiation, morphogenesis, and growth. Determination sets the developmental fate of a cell, which becomes more restrictive during development. Differentiation is the process by which specialized cells from less specialized cells such as stem cells.   Stem cells are undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell.  Cellular differentiation dramatically changes a cell's size, shape, membrane potential, metabolic activity, and responsiveness to signals, which are largely due to highly controlled modifications in gene expression and epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself.  Thus, different cells can have very different physical characteristics despite having the same genome. Morphogenesis, or development of body form, is the result of spatial differences in gene expression.  Specially, the organization of differentiated tissues into specific structures such as arms or wings, which is known as pattern formation, is governed by morphogens, signaling molecules that move from one group of cells to surrounding cells, creating a morphogen gradient as described by the French flag model. Apoptosis, or programmed cell death, also occurs during morphogenesis, such as the death of cells between digits in human embryonic development, which frees up individual fingers and toes. Expression of transcription factor genes can determine organ placement in a plant and a cascade of transcription factors themselves can establish body segmentation in a fruit fly. 
A small fraction of the genes in an organism's genome called the developmental-genetic toolkit control the development of that organism. These toolkit genes are highly conserved among phyla, meaning that they are ancient and very similar in widely separated groups of animals. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. Among the most important toolkit genes are the Hox genes. Hox genes determine where repeating parts, such as the many vertebrae of snakes, will grow in a developing embryo or larva.  Variations in the toolkit may have produced a large part of the morphological evolution of animals. The toolkit can drive evolution in two ways. A toolkit gene can be expressed in a different pattern, as when the beak of Darwin's large ground-finch was enlarged by the BMP gene,  or when snakes lost their legs as Distal-less (Dlx) genes became under-expressed or not expressed at all in the places where other reptiles continued to form their limbs.  Or, a toolkit gene can acquire a new function, as seen in the many functions of that same gene, distal-less, which controls such diverse structures as the mandible in vertebrates,   legs and antennae in the fruit fly,  and eyespot pattern in butterfly wings.  Given that small changes in toolbox genes can cause significant changes in body structures, they have often enabled convergent or parallel evolution.
A central organizing concept in biology is that life changes and develops through evolution, which is the change in heritable characteristics of populations over successive generations.   Evolution is now used to explain the great variations of life on Earth. The term evolution was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,  and fifty years later Charles Darwin and Alfred Russel Wallace formulated the theory of evolution by natural selection.     According to this theory, individuals differ from each other with respect to their heritable traits, resulting in different rates of survival and reproduction. As a results, traits that are better adapted to their environment are more likely to be passed on to subsequent generations.   Darwin was not aware of Mendel's work of inheritance and so the exact mechanism of inheritance that underlie natural selection was not well-understood  until the early 20th century when the modern synthesis reconciled Darwinian evolution with classical genetics, which established a neo-Darwinian perspective of evolution by natural selection.  This perspective holds that evolution occurs when there are changes in the allele frequencies within a population of interbreeding organisms. In the absence of any evolutionary process acting on a large random mating population, the allele frequencies will remain constant across generations as described by the Hardy–Weinberg principle. 
Another process that drives evolution is genetic drift, which is the random fluctuations of allele frequencies within a population from one generation to the next.  When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward at each successive generation because the alleles are subject to sampling error.  This drift halts when an allele eventually becomes fixed, either by disappearing from the population or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone.
Speciation is the process of splitting one lineage into two lineages that evolve independently from each other.  For speciation to occur, there has to be reproductive isolation.  Reproductive isolation can result from incompatibilities between genes as described by Bateson–Dobzhansky–Muller model. Reproductive isolation also tends to increase with genetic divergence. Speciation can occur when there are physical barriers that divide an ancestral species, a process known as allopatric speciation.  In contrast, sympatric speciation occurs in the absence of physical barriers.
Pre-zygotic isolation such as mechanical, temporal, behavioral, habitat, and gametic isolations can prevent different species from hybridizing.  Similarly, post-zygotic isolations can result in hybridization being selected against due to the lower viability of hybrids or hybrid infertility (e.g., mule). Hybrid zones can emerge if there were to be incomplete reproductive isolation between two closely related species.
A phylogeny is an evolutionary history of a specific group of organisms or their genes.  A phylogeny can be represented using a phylogenetic tree, which is a diagram showing lines of descent among organisms or their genes. Each line drawn on the time axis of a tree represents a lineage of descendents of a particular species or population. When a lineage divides into two, it is represented as a node (or split) on the phylogenetic tree. The more splits there are over time, the more branches there will be on the tree, with the common ancestor of all the organisms in that tree being represented by the root of that tree. Phylogenetic trees may portray the evolutionary history of all life forms, a major evolutionary group (e.g., insects), or an even smaller group of closely related species. Within a tree, any group of species designated by a name is a taxon (e.g., humans, primates, mammals, or vertebrates) and a taxon that consists of all its evolutionary descendants is a clade. Closely related species are referred to as sister species and closely related clades are sister clades.
Phylogenetic trees are the basis for comparing and grouping different species.  Different species that share a feature inherited from a common ancestor are described as having homologous features. Homologous features may be any heritable traits such as DNA sequence, protein structures, anatomical features, and behavior patterns. A vertebral column is an example of a homologous feature shared by all vertebrate animals. Traits that have a similar form or function but were not derived from a common ancestor are described as analogous features. Phylogenies can be reconstructed for a group of organisms of primary interests, which are called the ingroup. A species or group that is closely related to the ingroup but is phylogenetically outside of it is called the outgroup, which serves a reference point in the tree. The root of the tree is located between the ingroup and the outgroup.  When phylogenetic trees are reconstructed, multiple trees with different evolutionary histories can be generated. Based on the principle of Parsimony (or Occam's razor), the tree that is favored is the one with the fewest evolutionary changes needed to be assumed over all traits in all groups. Computational algorithms can be used to determine how a tree might have evolved given the evidence. 
Phylogeny provides the basis of biological classification, which is based on Linnaean taxonomy that was developed by Carl Linnaeus in the 18th century.  This classification system is rank-based, with the highest rank being the domain followed by kingdom, phylum, class, order, family, genus, and species.  All living organisms can be classified as belonging to one of three domains: Archaea (originally Archaebacteria) bacteria (originally eubacteria), or eukarya (includes the protist, fungi, plant, and animal kingdoms).  A binomial nomenclature is used to classify different species. Based on this system, each species is given two names, one for its genus and another for its species.  For example, humans are Homo sapiens, with Homo being the genus and sapiens being the species. By convention, the scientific names of organisms are italicized, with only the first letter of the genus capitalized.  
History of life
The history of life on Earth traces the processes by which organisms have evolved from the earliest emergence of life to present day. Earth formed about 4.5 billion years ago and all life on Earth, both living and extinct, descended from a last universal common ancestor that lived about 3.5 billion years ago.   The similarities among all known present-day species indicate that they have diverged through the process of evolution from their common ancestor.  Biologists regard the ubiquity of the genetic code as evidence of universal common descent for all bacteria, archaea, and eukaryotes.    
Microbal mats of coexisting bacteria and archaea were the dominant form of life in the early Archean Epoch and many of the major steps in early evolution are thought to have taken place in this environment.  The earliest evidence of eukaryotes dates from 1.85 billion years ago,   and while they may have been present earlier, their diversification accelerated when they started using oxygen in their metabolism. Later, around 1.7 billion years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions. 
Algae-like multicellular land plants are dated back even to about 1 billion years ago,  although evidence suggests that microorganisms formed the earliest terrestrial ecosystems, at least 2.7 billion years ago.  Microorganisms are thought to have paved the way for the inception of land plants in the Ordovician period. Land plants were so successful that they are thought to have contributed to the Late Devonian extinction event. 
Ediacara biota appear during the Ediacaran period,  while vertebrates, along with most other modern phyla originated about 525 million years ago during the Cambrian explosion.  During the Permian period, synapsids, including the ancestors of mammals, dominated the land,  but most of this group became extinct in the Permian–Triassic extinction event 252 million years ago.  During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates  one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods.  After the Cretaceous–Paleogene extinction event 66 million years ago killed off the non-avian dinosaurs,  mammals increased rapidly in size and diversity.  Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify. 
Bacteria and Archaea
Bacteria are a type of cell that constitute a large domain of prokaryotic microorganisms. Typically a few micrometers in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste,  and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. 
Archaea constitute the other domain of prokaryotic cells and were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), a term that has fallen out of use.  Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi.  Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes,  including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding unlike bacteria, no known species of Archaea form endospores.
The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.
Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin.  Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation nitrogen cycling organic compound turnover and maintaining microbial symbiotic and syntrophic communities, for example. 
Protists are eukaryotic organism that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor),  the exclusion of other eukaryotes means that protists do not form a natural group, or clade. [a] So some protists may be more closely related to animals, plants, or fungi than they are to other protists however, like algae, invertebrates, or protozoans, the grouping is used for convenience. 
The taxonomy of protists is still changing. Newer classifications attempt to present monophyletic groups based on morphological (especially ultrastructural),    biochemical (chemotaxonomy)   and DNA sequence (molecular research) information.   Because protists as a whole are paraphyletic, new systems often split up or abandon the kingdom, instead treating the protist groups as separate lines of eukaryotes.
Plants are mainly multicellular organisms, predominantly photosynthetic eukaryotes of the kingdom Plantae. Botany is the study of plant life, which would exclude fungi and some algae. Botanists have studied approximately 410,000 species of land plants of which some 391,000 species are vascular plants (including approximately 369,000 species of flowering plants),  and approximately 20,000 are bryophytes. 
Algae is a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga. Most are aquatic and autotrophic and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem, which are found in land plants. The largest and most complex marine algae are called seaweeds, while the most complex freshwater forms are the Charophyta.
Nonvascular plants are plants without a vascular system consisting of xylem and phloem. Instead, they may possess simpler tissues that have specialized functions for the internal transport of water. Vascular plants, on the other hand, are a large group of plants (c. 300,000 accepted known species)  that are defined as land plants with lignified tissues (the xylem) for conducting water and minerals throughout the plant.  They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).
Seed plants (or spermatophyte) comprise five divisions, four of which are grouped as gymnosperms and one is angiosperms. Gymnosperms includes conifers, cycads, Ginkgo, and gnetophytes. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or solitary as in yew, Torreya, Ginkgo.  Angiosperms are the most diverse group of land plants, with 64 orders, 416 families, approximately 13,000 known genera and 300,000 known species.  Like gymnosperms, angiosperms are seed-producing plants. They are distinguished from gymnosperms by having characteristics such as flowers, endosperm within their seeds, and production of fruits that contain the seeds.
Fungi are eukaryotic organisms that include microorganisms such as yeasts and molds, as well as the more familiar mushrooms. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), which share a common ancestor (from a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds).
Most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil or on dead matter. Fungi include symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange in the environment.
The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species.  Of these, only about 148,000 have been described,  with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. 
Animals are multicellular eukaryotic organisms that form the kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. They have complex interactions with each other and their environments, forming intricate food webs.
Sponges, the members of the phylum Porifera, are a basal Metazoa (animal) clade as a sister of the Diploblasts.      They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells.
97%) of animal species are invertebrates,  which are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snail, bivalves, squids, and octopuses), annelid (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals). Many invertebrate taxa have a greater number and variety of species than the entire subphylum of Vertebrata. 
In contrast, vertebrates comprise all species of animals within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.  Vertebrates include such groups as jawless fishes, jawed vertebrates such as cartilaginous fishes (sharks, rays, and ratfish), bony fishes, tetrapods such as amphibians, reptiles, birds and mammals.
Viruses are submicroscopic infectious agents that replicate inside the living cells of organisms.  Viruses infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.   More than 6,000 virus species have been described in detail.  Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity.  
When infected, a host cell is forced to rapidly produce thousands of identical copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or virions, consisting of the genetic material (DNA or RNA), a protein coat called capsid, and in some cases an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope, as they are one-hundredth the size of most bacteria.
The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity in a way analogous to sexual reproduction.  Because viruses possess some but not all characteristics of life, they have been described as "organisms at the edge of life",  and as self-replicators. 
Viruses can spread in many ways. One transmission pathway is through disease-bearing organisms known as vectors: for example, viruses are often transmitted from plant to plant by insects that feed on plant sap, such as aphids and viruses in animals can be carried by blood-sucking insects. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal–oral route, passed by hand-to-mouth contact or in food or water. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection.
Plant form and function
The plant body is made up of organs that can be organized into two major organ systems: a root system and a shoot system.  The root system anchors the plants into place. The roots themselves absorb water and minerals and store photosynthetic products. The shoot system is composed of stem, leaves, and flowers. The stems hold and orient the leaves to the sun, which allow the leaves to conduct photosynthesis. The flowers are shoots that have been modified for reproduction. Shoots are composed of phytomers, which are functional units that consist of a node carrying one or more leaves, internode, and one or more buds.
A plant body has two basic patterns (apical–basal and radial axes) that been established during embryogenesis.  Cells and tissues are arranged along the apical-basal axis from root to shoot whereas the three tissue systems (dermal, ground, and vascular) that make up a plant's body are arranged concentrically around its radial axis.  The dermal tissue system forms the epidermis (or outer covering) of a plant, which is usually a single cell layer that consists of cells that have differentiated into three specialized structures: stomata for gas exchange in leaves, trichomes (or leaf hair) for protection against insects and solar radiation, and root hairs for increased surface areas and absorption of water and nutrients. The ground tissue makes up virtually all the tissue that lies between the dermal and vascular tissues in the shoots and roots. It consists of three cell types: Parenchyma, collenchyma, and sclerenchyma cells. Finally, the vascular tissues are made up of two constituent tissues: xylem and phloem. The xylem is made up two of conducting cells called tracheids and vessel elements whereas the phloem is characterized by the presence of sieve tube elements and companion cells. 
Plant nutrition and transport
Like all other organisms, plants are primarily made up of water and other molecules containing elements that are essential to life.  The absence of specific nutrients (or essential elements), many of which have been identified in hydroponic experiments, can disrupt plant growth and reproduction. The majority of plants are able to obtain these nutrients from solutions that surrounds their roots in the soil.  Continuous leaching and harvesting of crops can deplete the soil of its nutrients, which can be restored with the use of fertilizers. Carnivorous plants such as Venus flytraps are able to obtain nutrients by digesting other arthropods whereas parasitic plants such as mistletoes can parasitize other plants for water and nutrients.
Plants need water to conduct photosynthesis, transport solutes between organs, cool their leaves by evaporation, and maintain internal pressures that support their bodies.  Water is able to diffuse in and out of plant cells by osmosis. The direction of water movement across a semipermeable membrane is determined by the water potential across that membrane.  Water is able to diffuse across a root cell's membrane through aquaporins whereas solutes are transported across by the membrane by ion channels and pumps. In vascular plants, water and solutes are able to enter the xylem, a vascular tissue, by way of an apoplast and symplast. Once in the xylem, the water and minerals are distributed upward by transpiration from the soil to the aerial parts of the plant.   In contrast, the phloem, another vascular tissue, distributes carbohydrates (e.g., sucrose) and other solutes such as hormones by translocation from a source (e.g., mature leaf or root) in which they were produced to a sink (e.g., root, flower, or developing fruit) in which they will be used and stored.  Sources and sinks can switch roles, depending on the amount of carbohydrates accumulated or mobilized for the nourishment of other organs.
Plant development is regulated by environmental cues and the plant's own receptors, hormones, and genome.  Morever, they have several characteristics that allow them to obtain resources for growth and reproduction such as meristems, post-embryonic organ formation, and differential growth.
Development begins with a seed, which is an embryonic plant enclosed in a protective outer covering. Most plant seeds are usually dormant, a condition in which the seed's normal activity is suspended.  Seed dormancy may last may last weeks, months, years, and even centuries. Dormancy is broken once conditions are favorable for growth, and the seed will begin to sprout, a process called germination. Imbibition is the first step in germination, whereby water is absorbed by the seed. Once water is absorbed, the seed undergoes metabolic changes whereby enzymes are activated and RNA and proteins are synthesized. Once the seed germinates, it obtains carbohydrates, amino acids, and small lipids that serve as building blocks for its development. These monomers are obtained from the hydrolysis of starch, proteins, and lipids that are stored in either the cotyledons or endosperm. Germination is completed once embryonic roots called radicle have emerged from the seed coat. At this point, the developing plant is called a seedling and its growth is regulated by its own photoreceptor proteins and hormones. 
Unlike animals in which growth is determinate, i.e., ceases when the adult state is reached, plant growth is indeterminate as it is an open-ended process that could potentially be lifelong.  Plants grow in two ways: primary and secondary. In primary growth, the shoots and roots are formed and lengthened. The apical meristem produces the primary plant body, which can be found in all seed plants. During secondary growth, the thickness of the plant increases as the lateral meristem produces the secondary plant body, which can be found in woody eudicots such as trees and shrubs. Monocots do not go through secondary growth.  The plant body is generated by a hierarchy of meristems. The apical meristems in the root and shoot systems give rise to primary meristems (protoderm, ground meristem, and procambium), which in turn, give rise to the three tissue systems (dermal, ground, and vascular).
Most angiosperms (or flowering plants) engage in sexual reproduction.  Their flowers are organs that facilitate reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate two types of pollination: self-pollination and cross-pollination. Self-pollination occurs when the pollen from the anther is deposited on the stigma of the same flower, or another flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one flower to the stigma of another flower on a different individual of the same species. Self-pollination happened in flowers where the stamen and carpel mature at the same time, and are positioned so that the pollen can land on the flower’s stigma. This pollination does not require an investment from the plant to provide nectar and pollen as food for pollinators. 
Like animals, plants produce hormones in one part of its body to signal cells in another part to respond. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.
To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.
Many plant organs contain different types of photoreceptor proteins, each of which reacts very specifically to certain wavelengths of light.  The photoreceptor proteins relay information such as whether it is day or night, duration of the day, intensity of light available, and the source of light. Shoots generally grow towards light, while roots grow away from it, responses known as phototropism and skototropism, respectively. They are brought about by light-sensitive pigments like phototropins and phytochromes and the plant hormone auxin.  Many flowering plants bloom at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism.
In addition to light, plants can respond to other types of stimuli. For instance, plants can sense the direction of gravity to orient themselves correctly. They can respond to mechanical stimulation. 
Animal form and function
The cells in each animal body are bathed in interstitial fluid, which make up the cell's environment. This fluid and all its characteristics (e.g., temperature, ionic composition) can be described as the animal's internal environment, which is in contrast to the external environment that encompasses the animal's outside world.  Animals can be classified as either regulators or conformers. Animals such as mammals and birds are regulators as they are able to maintain a constant internal environment such as body temperature despite their environments changing. These animals are also described as homeotherms as they exhibit thermoregulation by keeping their internal body temperature constant. In contrast, animals such as fishes and frogs are conformers as they adapt their internal environment (e.g., body temperature) to match their external environments. These animals are also described as poikilotherms or ectotherms as they allow their body temperatures to match their external environments. In terms of energy, regulation is more costly than conformity as an animal expands more energy to maintain a constant internal environment such as increasing its basal metabolic rate, which is the rate of energy consumption.  Similarly, homeothermy is more costly than poikilothermy. Homeostasis is the stability of an animal's internal environment, which is maintained by negative feedback loops.  
The body size of terrestrial animals vary across different species but their use of energy does not scale linearly according to their size.  Mice, for example, are able to consume three times more food than rabbits in proportion to their weights as the basal metabolic rate per unit weight in mice is greater than in rabbits.  Physical activity can also increase an animal's metabolic rate. When an animal runs, its metabolic rate increases linearly with speed.  However, the relationship is non-linear in animals that swim or fly. When a fish swims faster, it encounters greater water resistance and so its metabolic rates increases exponential.  Alternatively, the relationship of flight speeds and metabolic rates is U-shaped in birds.  At low flight speeds, a bird must maintain a high metabolic rates to remain airborne. As it speeds up its flight, its metabolic rate decreases with the aid of air rapidly flows over its wings. However, as it increases in its speed even further, its high metabolic rates rises again due to the increased effort associated with rapid flight speeds. Basal metabolic rates can be measured based on an animal's rate of heat production.
Water and salt balance
An animal's body fluids have three properties: osmotic pressure, ionic composition, and volume.  Osmotic pressures determine the direction of the diffusion of water (or osmosis), which moves from a region where osmotic pressure (total solute concentration) is low to a region where osmotic pressure (total solute concentration) is high. Aquatic animals are diverse with respect to their body fluid compositions and their environments. For example, most invertebrate animals in the ocean have body fluids that are isosmotic with seawater. In contrast, ocean bony fishes have body fluids that are hyposmotic to seawater. Finally, freshwater animals have body fluids that are hyperosmotic to fresh water. Typical ions that can be found in an animal's body fluids are sodium, potassium, calcium, and chloride. The volume of body fluids can be regulated by excretion. Vertebrate animals have kidneys, which are excretory organs made up of tiny tubular structures called nephrons, which make urine from blood plasma. The kidneys' primary function is to regulate the composition and volume of blood plasma by selectively removing material from the blood plasma itself. The ability of xeric animals such as kangaroo rats to minimize water loss by producing urine that is 10-20 times concentrated than their blood plasma allows them to adapt in desert environments that receive very little precipitation. 
Nutrition and digestion
Animals are heterotrophs as they feed on other living organisms to obtain energy and organic compounds.  They are able to obtain food in three major ways such as targeting visible food objects, collecting tiny food particles, or depending on microbes for critical food needs. The amount of energy stored in food can be quantified based on the amount of heat (measured in calories or kilojoules) emitted when the food is burnt in the presence of oxygen. If an animal were to consume food that contains an excess amount of chemical energy, it will store most of that energy in the form of lipids for future use and some of that energy as glycogen for more immediate use (e.g., meeting the brain's energy needs).  The molecules in food are chemical building blocks that are needed for growth and development. These molecules include nutrients such as carbohydrates, fats, and proteins. Vitamins and minerals (e.g., calcium, magnesium, sodium, and phosphorus) are also essential. The digestive system, which typically consist of a tubular tract that extends from the mouth to the anus, is involved in the breakdown (or digestion) of food into small molecules as it travels down peristaltically through the gut lumen shortly after it has been ingested. These small food molecules are then absorbed into the blood from the lumen, where they are then distributed to the rest of the body as building blocks (e.g., amino acids) or sources of energy (e.g., glucose). 
In addition to their digestive tracts, vertebrate animals have accessory glands such as a liver and pancreas as part of their digestive systems.  The processing of food in these animals begins in the foregut, which includes the mouth, esophagus, and stomach. Mechanical digestion of food starts in the mouth with the esophagus serving as a passageway for food to reach the stomach, where it is stored and disintegrated (by the stomach's acid) for further processing. Upon leaving the stomach, food enters into the midgut, which is the first part of the intestine (or small intestine in mammals) and is the principal site of digestion and absorption. Food that does not get absorbed are stored as indigestible waste (or feces) in the hindgut, which is the second part of the intestine (or large intestine in mammals). The hindgut then completes the reabsorption of needed water and salt prior to eliminating the feces from the rectum. 
The respiratory system consists of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies greatly, depending on the size of the organism, the environment in which it lives and its evolutionary history. In land animals the respiratory surface is internalized as linings of the lungs.  Gas exchange in the lungs occurs in millions of small air sacs in mammals and reptiles these are called alveoli, and in birds they are known as atria. These microscopic air sacs have a very rich blood supply, thus bringing the air into close contact with the blood.  These air sacs communicate with the external environment via a system of airways, or hollow tubes, of which the largest is the trachea, which branches in the middle of the chest into the two main bronchi. These enter the lungs where they branch into progressively narrower secondary and tertiary bronchi that branch into numerous smaller tubes, the bronchioles. In birds the bronchioles are termed parabronchi. It is the bronchioles, or parabronchi that generally open into the microscopic alveoli in mammals and atria in birds. Air has to be pumped from the environment into the alveoli or atria by the process of breathing which involves the muscles of respiration.
A circulatory system usually consists of a muscular pump such as a heart, a fluid (blood), and system of blood vessels that deliver it.   Its principal function is to transport blood and other substances to and from cell (biology)s and tissues. There are two types of circulatory systems: open and closed. In open circulatory systems, blood exits blood vessels as it circulates throughout the body whereas in closed circulatory system, blood is contained within the blood vessels as it circulates. Open circulatory systems can be observed in invertebrate animals such as arthropods (e.g., insects, spiders, and lobsters) whereas closed circulatory systems can be found in vertebrate animals such as fishes, amphibians, and mammals. Circulation in animals occur between two types of tissues: systemic tissues and breathing (or pulmonary) organs.  Systemic tissues are all the tissues and organs that make up an animal's body other than its breathing organs. Systemic tissues take up oxygen but adds carbon dioxide to the blood whereas a breathing organs takes up carbon dioxide but add oxygen to the blood.  In birds and mammals, the systemic and pulmonary systems are connected in series.
In the circulatory system, blood is important because it is the means by which oxygen, carbon dioxide, nutrients, hormones, agents of immune system, heat, wastes, and other commodities are transported.  In annelids such as earthworms and leeches, blood is propelled by peristaltic waves of contractions of the heart muscles that make up the blood vessels. Other animals such as crustaceans (e.g., crayfish and lobsters), have more than one heart to propel blood throughout their bodies. Vertebrate hearts are multichambered and are able to pump blood when their ventricles contract at each cardiac cycle, which propels blood through the blood vessels.  Although vertebrate hearts are myogenic, their rate of contraction (or heart rate) can be modulated by neural input from the body's autonomic nervous system.
Muscle and movement
In vertebrates, the muscular system consists of skeletal, smooth and cardiac muscles. It permits movement of the body, maintains posture and circulates blood throughout the body.  Together with the skeletal system, it forms the musculoskeletal system, which is responsible for the movement of vertebrate animals.  Skeletal muscle contractions are neurogenic as they require synaptic input from motor neurons. A single motor neuron is able to innervate multiple muscle fibers, thereby causing the fibers to contract at the same time. Once innervated, the protein filaments within each skeletal muscle fiber slide past each other to produce a contraction, which is explained by the sliding filament theory. The contraction produced can be described as a twitch, summation, or tetanus, depending on the frequency of action potentials. Unlike skeletal muscles, contractions of smooth and cardiac muscles are myogenic as they are initiated by the smooth or heart muscle cells themselves instead of a motor neuron. Nevertheless, the strength of their contractions can be modulated by input from the autonomic nervous system. The mechanisms of contraction are similar in all three muscle tissues.
In invertebrates such as earthworms and leeches, circular and longitudinal muscles cells form the body wall of these animals and are responsible for their movement.  In an earthworm that is moving through a soil, for example, contractions of circular and longitudinal muscles occur reciprocally while the coelomic fluid serves as a hydroskeleton by maintaining turgidity of the earthworm.  Other animals such as mollusks, and nematodes, possess obliquely striated muscles, which contain bands of thick and thin filaments that are arranged helically rather than transversely, like in vertebrate skeletal or cardiac muscles.  Advanced insects such as wasps, flies, bees, and beetles possess asynchronous muscles that constitute the flight muscles in these animals.  These flight muscles are often called fibrillar muscles because they contain myofibrils that are thick and conspicuous. 
The nervous system is a network of cells that processes sensory information and generates behaviors. At the cellular level, the nervous system is defined by the presence of neurons, which are cells specialized to handle information.  They can transmit or receive information at sites of contacts called synapses.  More specifically, neurons can conduct nerve impulses (or action potentials) that travel along their thin fibers called axons, which can then be transmitted directly to a neighboring cell through electrical synapses or cause chemicals called neurotransmitters to be released at chemical synapses. According to the sodium theory, these action potentials can be generated by the increased permeability of the neuron's cell membrane to sodium ions.  Cells such as neurons or muscle cells may be excited or inhibited upon receiving a signal from another neuron. The connections between neurons can form neural pathways, neural circuits, and larger networks that generate an organism's perception of the world and determine its behavior. Along with neurons, the nervous system contains other specialized cells called glia or glial cells, which provide structural and metabolic support.
Nervous systems are found in most multicellular animals, but vary greatly in complexity.  In vertebrates, the nervous system consists of the central nervous system (CNS), which includes the brain and spinal cord, and the peripheral nervous system (PNS), which consists of nerves that connect the CNS to every other part of the body. Nerves that transmit signals from the CNS are called motor nerves or efferent nerves, while those nerves that transmit information from the body to the CNS are called sensory nerves or afferent nerves. Spinal nerves are mixed nerves that serve both functions. The PNS is divided into three separate subsystems, the somatic, autonomic, and enteric nervous systems. Somatic nerves mediate voluntary movement. The autonomic nervous system is further subdivided into the sympathetic and the parasympathetic nervous systems. The sympathetic nervous system is activated in cases of emergencies to mobilize energy, while the parasympathetic nervous system is activated when organisms are in a relaxed state. The enteric nervous system functions to control the gastrointestinal system. Both autonomic and enteric nervous systems function involuntarily. Nerves that exit directly from the brain are called cranial nerves while those exiting from the spinal cord are called spinal nerves.
Many animals have sense organs that can detect their environment. These sense organs contain sensory receptors, which are sensory neurons that convert stimuli into electrical signals.  Mechanoreceptors, for example, which can be found in skin, muscle, and hearing organs, generate action potentials in response to changes in pressures.   Photoreceptor cells such as rods and cones, which are part of the vertebrate retina, can respond to specific wavelengths of light.   Chemoreceptors detect chemicals in the mouth (taste) or in the air (smell). 
Hormones are signaling molecules transported in the blood to distant organs to regulate their function.   Hormones are secreted by internal glands that are part of an animal's endocrine system. In vertebrates, the hypothalamus is the neural control center for all endocrine systems. In humans specifically, the major endocrine glands are the thyroid gland and the adrenal glands. Many other organs that are part of other body systems have secondary endocrine functions, including bone, kidneys, liver, heart and gonads. For example, kidneys secrete the endocrine hormone erythropoietin. Hormones can be amino acid complexes, steroids, eicosanoids, leukotrienes, or prostaglandins.  The endocrine system can be contrasted to both exocrine glands, which secrete hormones to the outside of the body, and paracrine signaling between cells over a relatively short distance. Endocrine glands have no ducts, are vascular, and commonly have intracellular vacuoles or granules that store their hormones. In contrast, exocrine glands, such as salivary glands, sweat glands, and glands within the gastrointestinal tract, tend to be much less vascular and have ducts or a hollow lumen.
Animals can reproduce in one of two ways: asexual and sexual. Nearly all animals engage in some form of sexual reproduction.  They produce haploid gametes by meiosis. The smaller, motile gametes are spermatozoa and the larger, non-motile gametes are ova.  These fuse to form zygotes,  which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, and develop into a new sponge.  In most other groups, the blastula undergoes more complicated rearrangement.  It first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm.  In most cases, a third germ layer, the mesoderm, also develops between them.  These germ layers then differentiate to form tissues and organs.  Some animals are capable of asexual reproduction, which often results in a genetic clone of the parent. This may take place through fragmentation budding, such as in Hydra and other cnidarians or parthenogenesis, where fertile eggs are produced without mating, such as in aphids.  
Animal development begins with the formation of a zygote that results from the fusion of a sperm and egg during fertilization.  The zygote undergoes a rapid multiple rounds of mitotic cell period of cell divisions called cleavage, which forms a ball of similar cells called a blastula. Gastrulation occurs, whereby morphogenetic movements convert the cell mass into a three germ layers that comprise the ectoderm, mesoderm and endoderm.
The end of gastrulation signals the beginning of organogenesis, whereby the three germ layers form the internal organs of the organism.  The cells of each of the three germ layers undergo differentiation, a process where less-specialized cells become more-specialized through the expression of a specific set of genes. Cellular differentiation is influenced by extracellular signals such as growth factors that are exchanged to adjacent cells, which is called juxtracrine signaling, or to neighboring cells over short distances, which is called paracrine signaling.   Intracellular signals consist of a cell signaling itself (autocrine signaling), also play a role in organ formation. These signaling pathways allows for cell rearrangement and ensures that organs form at specific sites within the organism.  
The immune system is a network of biological processes that detects and responds to a wide variety of pathogens. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.
Nearly all organisms have some kind of immune system. Bacteria have a rudimentary immune system in the form of enzymes that protect against virus infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.
Behaviors play a central a role in animals' interaction with each other and with their environment.  They are able to use their muscles to approach one another, vocalize, seek shelter, and migrate. An animal's nervous system activates and coordinates its behaviors. Fixed action patterns, for instance, are genetically determined and stereotyped behaviors that occur without learning.   These behaviors are under the control of the nervous system and can be quite elaborate.  Examples include the pecking of kelp gull chicks at the red dot on their mother's beak. Other behaviors that have emerged as a result of natural selection include foraging, mating, and altruism.  In addition to evolved behavior, animals have evolved the ability to learn by modifying their behaviors as a result of early individual experiences. 
Ecology is the study of the distribution and abundance of living organisms, the interaction between them and their environment.  The community of living (biotic) organisms in conjunction with the nonliving (abiotic) components (e.g., water, light, radiation, temperature, humidity, atmosphere, acidity, and soil) of their environment is called an ecosystem.    These biotic and abiotic components are linked together through nutrient cycles and energy flows.  Energy from the sun enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present. By breaking down dead organic matter, decomposers release carbon back to the atmosphere and facilitate nutrient cycling by converting nutrients stored in dead biomass back to a form that can be readily used by plants and other microbes. 
The Earth's physical environment is shaped by solar energy and topography.  The amount of solar energy input varies in space and time due to the spherical shape of the Earth and its axial tilt. Variation in solar energy input drives weather and climate patterns. Weather is the day-to-day temperature and precipitation activity, whereas climate is the long-term average of weather, typically averaged over a period of 30 years.   Variation in topography also produces environmental heterogeneity. On the windward side of a mountain, for example, air rises and cools, with water changing from gaseous to liquid or solid form, resulting in precipitation such as rain or snow.  As a result, wet environments allow for lush vegetation to grow. In contrast, conditions tend to be dry on the leeward side of a mountain due to the lack of precipitation as air descends and warms, and moisture remains as water vapor in the atmosphere. Temperature and precipitation are the main factors that shape terrestrial biomes.
A population is the number of organisms of the same species that occupy an area and reproduce from generation to generation.      Its abundance can be measured using population density, which is the number of individuals per unit area (e.g., land or tree) or volume (e.g., sea or air).  Given that it is usually impractical to count every individual within a large population to determine its size, population size can be estimated by multiplying population density by the area or volume. Population growth during short-term intervals can be determined using the population growth rate equation, which takes into consideration birth, death, and immigration rates. In the longer term, the exponential growth of a population tends to slow down as it reaches its carrying capacity, which can be modeled using the logistic equation.  The carrying capacity of an environment is the maximum population size of a species that can be sustained by that specific environment, given the food, habitat, water, and other resources that are available.  The carrying capacity of a population can be affected by changing environmental conditions such as changes in the availability resources and the cost of maintaining them. In human populations, new technologies such as the Green revolution have helped increase the Earth's carrying capacity for humans over time, which has stymied the attempted predictions of impending population decline, the famous of which was by Thomas Malthus in the 18th century. 
A community is a group of populations of two or more different species occupying the same geographical area at the same time. A biological interaction is the effect that a pair of organisms living together in a community have on each other. They can be either of the same species (intraspecific interactions), or of different species (interspecific interactions). These effects may be short-term, like pollination and predation, or long-term both often strongly influence the evolution of the species involved. A long-term interaction is called a symbiosis. Symbioses range from mutualism, beneficial to both partners, to competition, harmful to both partners. 
Every species participates as a consumer, resource, or both in consumer–resource interactions, which form the core of food chains or food webs.  There are different trophic levels within any food web, with the lowest level being the primary producers (or autotrophs) such as plants and algae that convert energy and inorganic material into organic compounds, which can then be used by the rest of the community.    At the next level are the heterotrophs, which are the species that obtain energy by breaking apart organic compounds from other organisms.  Heterotrophs that consume plants are primary consumers (or herbivores) whereas heterotrophs that consume herbivores are secondary consumers (or carnivores). And those that eat secondary consumers are tertiary consumers and so on. Omnivorous heterotrophs are able to consume at multiple levels. Finally, there are decomposers that feed on the waste products or dead bodies of organisms. 
On average, the total amount of energy incorporated into the biomass of a trophic level per unit of time is about one-tenth of the energy of the trophic level that it consumes. Waste and dead material used by decomposers as well as heat lost from metabolism make up the other ninety percent of energy that is not consumed by the next trophic level. 
In the global ecosystem (or biosphere), matter exist as different interacting compartments, which can be biotic or abiotic as well as accessible or inaccessible, depending on their forms and locations.  For example, matter from terrestrial autotrophs are both biotic and accessible to other living organisms whereas the matter in rocks and minerals are abiotic and inaccessible to living organisms. A biogeochemical cycle is a pathway by which specific elements of matter are turned over or moved through the biotic (biosphere) and the abiotic (lithosphere, atmosphere, and hydrosphere) compartments of Earth. There are biogeochemical cycles for nitrogen, carbon, and water. In some cycles there are reservoirs where a substance remains or is sequestered for a long period of time.
Climate change includes both global warming driven by human-induced emissions of greenhouse gases and the resulting large-scale shifts in weather patterns. Though there have been previous periods of climatic change, since the mid-20th century humans have had an unprecedented impact on Earth's climate system and caused change on a global scale.  The largest driver of warming is the emission of greenhouse gases, of which more than 90% are carbon dioxide and methane.  Fossil fuel burning (coal, oil, and natural gas) for energy consumption is the main source of these emissions, with additional contributions from agriculture, deforestation, and manufacturing.  Temperature rise is accelerated or tempered by climate feedbacks, such as loss of sunlight-reflecting snow and ice cover, increased water vapor (a greenhouse gas itself), and changes to land and ocean carbon sinks.
Conservation biology is the study of the conservation of Earth's biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction and the erosion of biotic interactions.    It is concerned with factors that influence the maintenance, loss, and restoration of biodiversity and the science of sustaining evolutionary processes that engender genetic, population, species, and ecosystem diversity.     The concern stems from estimates suggesting that up to 50% of all species on the planet will disappear within the next 50 years,  which has contributed to poverty, starvation, and will reset the course of evolution on this planet.   Biodiversity affects the functioning of ecosystems, which provide a variety of services upon which people depend.
Conservation biologists research and educate on the trends of biodiversity loss, species extinctions, and the negative effect these are having on our capabilities to sustain the well-being of human society. Organizations and citizens are responding to the current biodiversity crisis through conservation action plans that direct research, monitoring, and education programs that engage concerns at local through global scales.    
Human pregnancy begins with fertilization of an egg and proceeds through the three trimesters of gestation. The labor process has three stages (contractions, delivery of the fetus, expulsion of the placenta), each propelled by hormones. The first trimester lays down the basic structures of the body, including the limb buds, heart, eyes, and the liver. The second trimester continues the development of all of the organs and systems. The third trimester exhibits the greatest growth of the fetus and culminates in labor and delivery. Prevention of a pregnancy can be accomplished through a variety of methods including barriers, hormones, or other means. Assisted reproductive technologies may help individuals who have infertility problems.