BIOL 1408 Course Guide

Which of the following statements is false?

1. Tissues exist within organs which exist within organ systems.
2. Communities exist within populations which exist within ecosystems.
3. Organelles exist within cells which exist within tissues.
4. Communities exist within ecosystems which exist in the biosphere.

-Adapted from Concepts of Biology by OpenStax is licensed under CC BY 4.0 (See 1.2 Themes and Concepts of Biology)
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All life on Earth evolved from a common ancestor. Biologists map how organisms are related by constructing phylogenetic trees. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms, as shown in Figure 12.2. Notice that from a single point, the three domains of Archaea, Bacteria, and Eukarya diverge and then branch repeatedly. The small branch that plants and animals (including humans) occupy in this diagram shows how recently these groups had their origin compared with other groups.

The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer. For example, in the most inclusive grouping, scientists divide organisms into three domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.

As an example, the classification levels for the domestic dog are shown in Figure 20.5.

-Adapted from Concepts of Biology by OpenStax is licensed under CC BY 4.0  (See 12.1 Organizing Life on Earth)
-Figure 20.5 from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 20.1 Organizing Life on Earth)

Acids, Bases, pH and Buffers

The pH of a solution is a measure of its acidity or bascicity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (basicity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale (Figure 2.12). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.

The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).

Acids are substances that provide hydrogen ions (H⁺) and lower pH, whereas bases provide hydroxide ions (OH^–) and raise pH. The stronger the acid, the more readily it donates H⁺. For example, hydrochloric acid and lemon juice are very acidic and readily give up H⁺ when added to water. Conversely, bases are those substances that readily donate OH^–. The OH^– ions combine with H⁺ to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up OH^– rapidly when placed in water, thereby raising the pH.

Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.

So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffers readily absorb excess H⁺ or OH^–, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H₂CO₃) and bicarbonate (HCO₃^–) anion. If too much H⁺ enters the body, bicarbonate will combine with the H⁺ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH^– is introduced into the system, carbonic acid will rapidly dissociate into bicarbonate and H⁺ ions. The H⁺ ions can combine with the OH^– ions, limiting the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.

-Adapted from Concepts of Biology by OpenStax is licensed under CC BY 4.0  (See 2.2 Water)
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Biological Molecules

Key Terms

Biological macromolecule - A large, organic molecule such as carbohydrates, lipids, proteins, and nucleic acids.

Monomer - A molecule that is a building block for larger molecules (polymers). For example, an amino acid acts as the building blocks for proteins.

Polymer - A large molecule made of repeating subunits (monomers). For example, a carbohydrate is a polymer that is made of repeating monosaccharides.

-Adapted from Biological macromolecules review by Khan Academy is licensed under CC BY-NC-SA 3.0. All Khan Academy content is available for free at www.khanacademy.org.

Osmosis is the movement of water through a semipermeable membrane according to the water's concentration gradient across the membrane, which is inversely proportional to the solutes' concentration. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the solutes' diffusion in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules.

In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the cell's osmolarity matches that of the extracellular fluid, there will be no net movement of water into or out of the cell, although water will still move in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure 5.12).

A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0 (See 5.2 Passive Transport)
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Primary Active Transport

The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still active because it depends on using energy as does primary transport (Figure 5.18).

One of the most important pumps in animal cells is the sodium-potassium pump (Na⁺-K⁺ ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na⁺ and K⁺) in living cells. The sodium-potassium pump moves K⁺ into the cell while moving Na⁺ out at the same time, at a ratio of three Na⁺ for every two K⁺ ions moved in. The Na⁺-K⁺ ATPase exists in two forms, depending on its orientation to the cell's interior or exterior and its affinity for either sodium or potassium ions. The process consists of the following six steps.

1. With the enzyme oriented towards the cell's interior, the carrier has a high affinity for sodium ions. Three ions bind to the protein.
2. The protein carrier hydrolyzes ATP and a low-energy phosphate group attaches to it.
3. As a result, the carrier changes shape and reorients itself towards the membrane's exterior. The protein’s affinity for sodium decreases and the three sodium ions leave the carrier.
4. The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier.
5. With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the cell's interior.
6. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions moves into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again.

Several things have happened as a result of this process. At this point, there are more sodium ions outside the cell than inside and more potassium ions inside than out. For every three sodium ions that move out, two potassium ions move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.

Secondary Active Transport (Co-transport)

Secondary active transport uses the kinetic energy of the sodium ions to bring other compounds, against their concentration gradient into the cell. As sodium ion concentrations build outside of the plasma membrane because of the primary active transport process, this creates an electrochemical gradient. If a channel protein exists and is open, the sodium ions will move down its concentration gradient across the membrane. This movement transports other substances that must be attached to the same transport protein in order for the sodium ions to move across the membrane (Figure 5.19). Many amino acids, as well as glucose, enter a cell this way. This secondary process also stores high-energy hydrogen ions in the mitochondria of plant and animal cells in order to produce ATP. The potential energy that accumulates in the stored hydrogen ions translates into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy then converts ADP into ATP.

If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease?
 

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 5.3 Active Transport)
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On a hot, dry day, the guard cells of plants close their stomata to conserve water. What impact will this have on photosynthesis?

Two Part of Photosynthesis

Learn more about photosynthesis at Khan Academy link .

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 8.1 Overview of Photosynthesis)
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Karyokinesis (Mitosis)

Karyokinesis, also known as mitosis, is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 10.6).

Which of the following is the correct order of events in mitosis?

1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate.
2. The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides.
3. The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides.
4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides.

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 10.2 The Cell Cycle)
Access for free at https://openstax.org/books/biology-2e/pages/1-introduction

For further information, follow the link to mitosis.  * STC username and password required to access library database material from off campus.

The Process of Meiosis

Review the process of meiosis, observing how chromosomes align and migrate, at Meiosis: An Interactive Animation.

For further information, follow the link to meiosis. * STC Jagnet username and password required to access library database material from off campus.

Comparing Meiosis and Mitosis

Click through the steps of this interactive animation to compare the meiotic process of cell division to that of mitosis at How Cells Divide.

Visit Mitosis versus meiosis for further information on their differences and similarities.

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 11.1 The Process of Meiosis)
Access for free at https://openstax.org/books/biology-2e/pages/1-introduction

Mendel's Model System

Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.

Mendelian Crosses

Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes (sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes (ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendel painstakingly removed all of the anthers from the plant’s flowers before they had a chance to mature.

Plants used in first-generation crosses were called P₀, or parental generation one (Figure 12.3). After each cross, Mendel collected the seeds belonging to the P₀ plants and grew them the following season. These offspring were called the F₁, or the first filial (filial = offspring, daughter or son) generation. Once Mendel examined the characteristics in the F₁ generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F₁ plants to produce the F₂, or second filial, generation. Mendel’s experiments extended beyond the F₂ generation to the F₃ and F₄ generations, and so on, but it was the ratio of characteristics in the P₀−F₁−F₂ generations that were the most intriguing and became the basis for Mendel’s postulates.

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0 (See 12.1 Mendel's Experiments and the Laws of Probability)
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Miskevich, F. (2016). Microbiology. QuickStudy Reference Guides.  Link to see. * STC Jagnet username and password required to access library database material from off campus.

CRISPR stands for "Clustered Regularly Interspaced Short Palindromic Repeats." These are segments of prokaryotic DNA with short base sequences that are repeated over and over. Each repetition of the DNA is followed by spacer DNA, short segments of DNA that are left over from exposure to foreign DNA.

Cas-9 is an enzyme that is produced by CRISPR that can bind with DNA and cut it, thereby editing a gene.

CRISPR-Cas9 works by causing a mutation in the DNA of a cell. Cas9 acts like a pair of scissors that cuts DNA at a specific chosen location in the cell's DNA so that it can be changed or removed. Guide RNA (gRNA) is used to bind to the DNA and guide Cas9 to the previously selected part of the gene to make sure that Cas9 is cutting the DNA at the correct place. After Cas9 cuts across both strands of DNA, the cell recognizes that its DNA is damaged and begins to repair it. (Madsen, 2017, p.127)

Gene editing has great potential as a tool for helping people who have conditions that are genetically related...However, gene editing of reproductive cells has caused many people to question it. Any change made in reproductive cells will be passed on from generation to generation, causing people to wonder about the long-term implications and consequences. (Madsen, 2017, p. 128)

Madsen, M.M. (2017). CRISPR-Cas9. In C.A. Crawford (Ed.), Principles of Biology. Grey House Publishing.

For more info and an animation visit: What is CRISPR gene editing, and how does it work? *

For additional applications of CRISPR, see: CRISPR isn’t just for editing human embryos, it also works for plants and bugs: 5 essential reads *

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 The CRISPR Revolution
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Charles Darwin and Natural Selection

In the mid-nineteenth century, two naturalists, Charles Darwin and Alfred Russel Wallace, independently conceived and described the actual mechanism for evolution. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (Figure 18.2). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the South American mainland. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that each finch's varied beaks helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.

Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, or “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits. This leads to evolutionary change.

-Adapted from Biology 2e by OpenStax is licensed under CC BY 4.0  (See 18.1 Understanding Evolution)
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Microevolution

Microevolution is the process by which small changes in genotype frequencies occur in population over time. The study of microevolution is often referred to as population genetics.

Microevolution occurs because of the following factors:

• Mutations are the ultimate source of variation. Certain genotypic variations may be of evolutionary significance only if the environment changes. Genetic diversity is promoted when there are several alleles for each gene locus.
• Gene flow is the movement of alleles that occurs when breeding individuals migrate to another population.
• Nonrandom mating occurs when relatives mate (inbreeding) or when assortative mating takes place. Sexual selection, which occurs when a characteristic that increases the chances of mating is favored, promotes random mating.
• Genetic drift occurs when allele frequencies are altered by chance. Genetic drift may occur through a bottleneck effect or founder effect, both of which change the frequency of alleles in the gene pool.
• Natural selection.  (Mader & Windelspecht, 2018, p. 263.)

"Macroevolution represents "larger-scale changes in a population over very long periods of time...Macroevolution often results in speciation, or the formation of new species...speciation is due to changes in the gene pool and the divergence of two populations genetically, all of which is based on the principles of microevolution." (Mader & Windelspecht, 2018, p. 266.)

-Mader, S.S. & Windelspecht, M. (2018). Essentials of Biology (Fifth Edition). McGraw-Hill Education.

For additonal information, visit: Population Genomics/Macro vs Microevolution . *

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