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3.2: Introduction - Biology

3.2: Introduction - Biology


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The Earth formed around 4.54 billion years ago. Additionally, these early life forms were so small and simple that some argue the fossils are likely complex mineral structures, not organisms at all.

The earliest fossils are interpreted to be unicellular organisms similar to modern day cyanobacteria, sometimes referred to as blue green algae. The most widely accepted of these fossils dates back to 3.4 billion years ago from the Strelley Pool Formation in Western Australia. These particular fossils are called stromatolites and are composed of alternating layers of fossilized cells and calcium carbonate. We can use evidence from modern day stromatolite formation in Western Australia to infer that these fossilized cells were doing a process called photosynthesis, using dissolved CO2 in the water to form sugar molecules. This causes calcium to precipitate out of the seawater, forming hardened layers of calcium carbonate on top of the colony of organisms. Because they need access to light to continue photosynthesizing, living cells begin forming a new layer on top of the calcium carbonate. This process continues, making a ringed pattern as the formation grows, much like we see in trees and corals.


3.2 Carbohydrates

By the end of this section, you will be able to do the following:

  • Discuss the role of carbohydrates in cells and in the extracellular materials of animals and plants
  • Explain carbohydrate classifications
  • List common monosaccharides, disaccharides, and polysaccharides

Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have enough energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet. Grains, fruits, and vegetables are all natural carbohydrate sources that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.

Molecular Structures

The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates . In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (hence, “hydrate”). Scientists classify carbohydrates into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

Monosaccharides (mono- = “one” sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is a ketose. Depending on the number of carbons in the sugar, they can be trioses (three carbons), pentoses (five carbons), and/or hexoses (six carbons). Figure 3.4 illustrates monosaccharides.

The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of energy. During cellular respiration, energy releases from glucose, and that energy helps make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose in turn provides energy requirements for the plant. Humans and other animals that feed on plants often obtain glucose from catabolized (cell breakdown of larger molecules) starch.

Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are isomers) because of the different arrangement of functional groups around the asymmetric carbon. All these monosaccharides have more than one asymmetric carbon (Figure 3.5).

Visual Connection

What kind of sugars are these, aldose or ketose?

Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have the same chemical formula but have slightly different structures. Glucose and galactose are aldoses, and fructose is a ketose.

Monosaccharides can exist as a linear chain or as ring-shaped molecules. In aqueous solutions they are usually in ring forms (Figure 3.6). Glucose in a ring form can have two different hydroxyl group arrangements (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the ring formation process). If the hydroxyl group is below carbon number 1 in the sugar, it is in the alpha (α) position, and if it is above the plane, it is in the beta (β) position.

Disaccharides

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (or a condensation reaction or dehydration synthesis). During this process, one monosaccharide's hydroxyl group combines with another monosaccharide's hydrogen, releasing a water molecule and forming a covalent bond. A covalent bond forms between a carbohydrate molecule and another molecule (in this case, between two monosaccharides). Scientists call this a glycosidic bond (Figure 3.7). Glycosidic bonds (or glycosidic linkages) can be an alpha or beta type. An alpha bond is formed when the OH group on the carbon-1 of the first glucose is below the ring plane, and a beta bond is formed when the OH group on the carbon-1 is above the ring plane.

Common disaccharides include lactose, maltose, and sucrose (Figure 3.8). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is comprised of glucose and fructose monomers.

Polysaccharides

A long chain of monosaccharides linked by glycosidic bonds is a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more depending on the number of joined monomers. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.

Plants store sugars in the form of starch. In plants, an amylose and amylopectin mixture (both glucose polymers) comprise these sugars. Plants are able to synthesize glucose, and they store the excess glucose, beyond their immediate energy needs, as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a food source for humans and animals. Enzymes break down the starch that humans consume. For example, an amylase present in saliva catalyzes, or breaks down this starch into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.

Glucose starch comprises monomers that are joined by α 1-4 or α 1-6 glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As Figure 3.9 illustrates, unbranched glucose monomer chains (only α 1-4 linkages) form the starch whereas, amylopectin is a branched polysaccharide (α 1-6 linkages at the branch points).

Glycogen is the storage form of glucose in humans and other vertebrates and is comprised of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen breaks down to release glucose in a process scientists call glycogenolysis.

Cellulose is the most abundant natural biopolymer. Cellulose mostly comprises a plant's cell wall. This provides the cell structural support. Wood and paper are mostly cellulosic in nature. Glucose monomers comprise cellulose that β 1-4 glycosidic bonds link (Figure 3.10).

As Figure 3.10 shows, every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. While human digestive enzymes cannot break down the β 1-4 linkage, herbivores such as cows, koalas, and buffalos are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In some of these animals, certain species of bacteria and protists reside in the rumen (part of the herbivore's digestive system) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in ruminants' digestive systems. Cellulases can break down cellulose into glucose monomers that animals use as an energy source. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases.

Carbohydrates serve various functions in different animals. Arthropods (insects, crustaceans, and others) have an outer skeleton, the exoskeleton, which protects their internal body parts (as we see in the bee in Figure 3.11). This exoskeleton is made of the biological macromolecule chitin , which is a nitrogen-containing polysaccharide. It is made of repeating N-acetyl-β-d-glucosamine units, which are a modified sugar. Chitin is also a major component of fungal cell walls. Fungi are neither animals nor plants and form a kingdom of their own in the domain Eukarya.

Career Connection

Registered Dietitian

Obesity is a worldwide health concern, and many diseases such as diabetes and heart disease are becoming more prevalent because of obesity. This is one of the reasons why people increasingly seek out registered dietitians for advice. Registered dietitians help plan nutrition programs for individuals in various settings. They often work with patients in health care facilities, designing nutrition plans to treat and prevent diseases. For example, dietitians may teach a patient with diabetes how to manage blood sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices.

To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and physiology (biological functions) of food (proteins, carbohydrates, and fats).

Benefits of Carbohydrates

Are carbohydrates good for you? Some people believe that carbohydrates are bad and they should avoid them. Some diets completely forbid carbohydrate consumption, claiming that a low-carbohydrate diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years. Artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors’ storage areas.

As part of a well balanced diet, we should supplement carbohydrates with proteins, vitamins, and fats. Calorie-wise, a gram of carbohydrate provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable ratio. Carbohydrates contain soluble and insoluble elements. The insoluble part, fiber, is mostly cellulose. Fiber has many uses. It promotes regular bowel movement by adding bulk, and it regulates the blood glucose consumption rate. Fiber also helps to remove excess cholesterol from the body. Fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream. Cholesterol then exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, glucose breaks down during the cellular respiration process, which produces ATP, the cell's energy currency. Without consuming carbohydrates, we reduce the availability of “instant energy”. Eliminating carbohydrates from the diet may be necessary for some people, but such a step may not be healthy for everyone.

Link to Learning

For an additional perspective on carbohydrates, explore “Biomolecules: the Carbohydrates” through this interactive animation.


Undergraduate Biology (BIOL) Courses

1106/BIOL 1106 Principles of Biology I Laboratory (0-3). Laboratory designed to reinforce lecture topics of Biology 1306 and develop analytical skills essential to the practice of biology. Students must register for Biology 1306 concurrently. Recommended as a second semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1107/BIOL 1107 Principles of Biology II Laboratory (0-3). Laboratory designed to reinforce lecture topics of Biology 1307 and develop analytical skills essential to the practice of biology. Students must register for Biology 1307 concurrently. Recommended as a first semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1108/BIOL 1108 Human Biology Laboratory (0-2). Laboratory designed to reinforce lecture topics of Biology 1308. Co-registration for Biology 1308 is suggested. Not intended for Biology majors.

1109/BIOL 1109 Man and the Environment Laboratory (0-2). Laboratory designed to reinforce lecture topics of Biology 1309. Co-registration for Biology1309 is suggested. Not intended for Biology majors.

1306/BIOL 1306 Principles of Biology I (3-0). An introduction to the unifying principles of biology with emphasis on biological chemistry, energetics and homeostasis, cell structure and function, gene expression, and patterns of inheritance. Students must register for Biology 1106 concurrently. Recommended as a second semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1307/BIOL 1307 Principles of Biology II (3-0). An introduction to the unifying principles of biology with emphasis on biological diversity, evolution, and ecology. Students must register for Biology 1107 concurrently. Recommended as a first semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1308/BIOL 1308 Human Biology (3-0). An introductory owner’s manual to the human body for nonbiology majors. Includes fundamentals of human anatomy and the functions of the major systems of the body, contemporary health issues, human heredity, and human evolution. Co-registration for Biology 1108 is suggested.

1309/BIOL 1309 Man and the Environment (3-0). A introductory owner’s manual to Earth for nonbiology majors. Includes a survey of contemporary ecological concepts that affect man’s life, values, and culture. Topics include the biosphere and ecosystems, adaptation, environmental pollution, waste management, conservation, population growth, and world food problems. Co-registration for Biology 1109 is suggested. Not intended for Biology majors.

1406/BIOL 1406 Principles of Biology I (3-3). An introduction to the unifying principles of biology with emphasis on biological chemistry, energetics and homeostasis, cell structure and function, gene expression, and patterns of inheritance. Laboratory is designed to reinforce lecture topics and develop analytical skills essential to the practice of biology. Recommended as a second semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1407/BIOL 1407 Principles of Biology II (3-3). An introduction to the unifying principles of biology with emphasis on biological diversity, evolution, and ecology. Laboratory is designed to reinforce lecture topics and develop analytical skills essential to the practice of biology. Recommended as a first semester course of a two-course sequence for students majoring in biological sciences or related disciplines. Not intended for non-majors.

1408/BIOL 1408 Human Biology (3-2). An introductory owner’s manual to the human body for nonbiology majors. Includes fundamentals of human anatomy and the functions of the major systems of the body, contemporary health issues, human heredity, and human evolution.

1409/BIOL 1409 Man and the Environment (3-2). A introductory owner’s manual to Spaceship Earth for nonbiology majors. Includes a survey of contemporary ecological concepts that affect man’s life, values, and culture. Topics include the biosphere and ecosystems, adaptation, environmental pollution, waste management, conservation, population growth, and world food problems.

1411/BIOL 1411 General Botany (3-3). A consideration of the structural adaptations and diversity of plants and their life cycles. Laboratory will emphasize classification and comparative anatomy of the Kingdoms Fungi and Plantae.
Prerequisite: Credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107).

1413/BIOL 1413 General Zoology (3-3). A consideration of the structural adaptations of animals. Laboratory will emphasize classification and comparative anatomy within the Kingdom Animalia.
Prerequisite: Credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107).

2123 Human Anatomy Laboratory (0-3). Laboratory designed to reinforce lecture topics of Biology 2323. Students must register for Biology 2323 concurrently.

2124 Human Physiology Laboratory (0-3). Laboratory designed to reinforce lecture topics of Biology 2324. Students must register for Biology 2324 concurrently

2320 Medical Terminology (3-0). Study of common medical terminology used in oral and written communications in the health professions. Terminology describing anatomical, physiological, and pathological conditions will be studied, including those used in diagnostic procedures and treatments. Special emphasis on root words, medical prefixes and suffixes, pronunciation, abbreviations, and symbols.

2323 Human Anatomy (3-0). The study of the structure of cells, tissues, organs, and systems of the human body. Students must register for Biology 2123 concurrently.

2324 Human Physiology (3-0). The study of the normal functions of the cells, tissues, organs, and systems of the human body. Students must register for Biology 2124 concurrently.
Prerequisite: Credit for Biology 2323 or 2423.

2403 Comparative Plant and Animal Physiology (3-3). A general introduction to how plants and animals function, comparative in approach and stressing the principles of physiology which govern the degree of environmental adaptation.
Prerequisites: Biology 1411, 1413.

2406/BIOL 2406 Environmental Biology (3-3). Principles of environmental systems and ecology, including biogeochemical cycles, energy transformations, abiotic interactions, symbiotic relationships, natural resources and their management, lifestyle analysis, evolutionary trends, hazards and risks, and approaches to ecological research. Does not apply toward the biology minor or major.

2420/BIOL 2420 Microbiology for Non-Science Majors (3-2). The study of infectious disease processes including host-microbe interactions and medical intervention. Laboratory includes basic microbiological methodology and case studies.
Prerequisites: Biology 2323/2123 or Health Science Professions 2301/2101 Biology 2324/2124 or Health Science Professions 2302/2102 are recommended.

2423 Human Anatomy (3-3). The study of the structure of cells, tissues, organs, and systems of the human body.

2424 Human Physiology (3-3). The study of the normal functions of the cells, tissues, organs, and systems of the human body.
Prerequisite: Credit for Biology 2323/2123.

3101 Genetics Laboratory (0-2). Computer based problem solving in genetics. Optional laboratory to accompany Biology 3301.
Prerequisite: Concurrent enrollment or credit in Biology 3301.

3301 Genetics (3-0). This is a course in general genetics. Topics are organized into three major areas: cytogenetics, molecular genetics and classical genetics.
Prerequisite: Credit for Biology 1306/1106 and 1307/1107, or Biology 2323/2123 and 2324/2124, with a grade of 𠇌” or better.

3302 Medical Genetics (3-0). A study of the role of genetics in human health with emphasis placed upon the mechanisms, methods of diagnosis and current treatment of genetic diseases. Course work will involve case studies and problem sets and will include learning to use a computer data base to retrieve information on human genetic diseases.
Prerequisite: Must have completed Biology 3301 with a grade of 𠇊”.

3305 Medical Botany (3-0). An introduction to pharmacognosy and humanistic botany, including a discussion of the major food plants, special medicinal plants, plant hallucinogens, poisonous plants, and other economically important plants.
Prerequisite: Credit for one semester of biology or consent of instructor.

3333 Natural History of the Concho Valley (3-0). A study of the relationship among geology, soils, climate, plants, animals, and recent human history in the Concho Valley region of Texas. Emphasis will be placed on understanding woody vegetation and vertebrate animals of the region.

3403 Cell Biology (3-3). Study of the morphology, function, biochemistry and molecular biology of cells and organelles. Laboratory work will involve the practice and application of techniques to cell biology.
Prerequisites: Biology 1306/1106, 3301, and two semesters of chemistry.

3411 General Microbiology (3-3). The major areas in the field of microbiology are surveyed, with special emphasis given to the bacteria. Groups of microorganisms are characterized in sufficient detail to reveal their nature. Fundamental concepts of biology and basic biological processes common to all forms of life are emphasized. Laboratory methods are stressed, and detailed studies are made of pure cultures.
Prerequisite: Credit for Biology 1306/1106 and 1307/1107, or Biology 2323/2123 and 2324/2124, with a grade of 𠇌” or better.

3412 Pathogenic Microbiology (3-3). The relationship of microorganisms to human disease with an emphasis on bacteria. Elements of immunity and diagnosis and treatment of infection will be covered. This course includes a heavy emphasis on the role and application of laboratory work.
Prerequisites: Any three of the following courses each with a grade of 𠇌” or better: Biology 1306/1106, 1307/1107, 1411, 1413, 3301, 3411, or by special departmental approval.

3413 Immunology (3-2). A study of the specific cellular and humoral responses of the animal body to microorganisms and certain other extrinsic and intrinsic agents.
Prerequisites: Any three of the following courses each with a grade of 𠇌” or better: Biology 1306/1106, 1307/1107, 1411, 1413, 3301, 3411 or 3412, or by special departmental approval.

3421 Histology (3-3). The microscopic study of normal cells, tissues, organs, and systems of the human body with emphasis on integration of microscopic structure with physiology, embryology, and other areas of biology.
Prerequisites: Credit for two courses in biology for majors (Biology 1306/1106, 1307/1107, 1411, 1413), or (Biology 2323/2123 and 2324/2124).

3461 Entomology (3-3). General entomology: a survey of the important orders and families of insects with emphasis on the natural history, systematics, taxonomy, and physiology of the group. Laboratory will include field trips with required collection and identification of local representative taxa.
Prerequisite: Biology 1413 or consent of instructor.

4061 Internship: Credit 1 to 6. A supervised course providing practical on-the-job experience in the student’s major. Grading will be either pass or fail.
Prerequisites: Sophomore standing and approval of department chair. 3.00 or better GPA in major and overall.

4181 Seminar in Biology (1-0). A course designed to acquaint the student with the basic literature of the discipline and to encourage an exchange among biology majors and faculty members on selected topics.

4191, 4291, 4391 Research. Individual research problems for superior students majoring in biology. (May be repeated to a total of six semester hours credit.)
Prerequisites: Junior standing. Approval from the Chair of the Department is required prior to enrollment.

4301 Conservation Biology (3-0). Theory and practice of conservation biology with emphasis on the maintenance of species diversity, factors affecting extinction, genetic impacts of rarity, and practical management considerations, including design of reserves and captive breeding and release programs.
Prerequisites: Credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107, 1480) and Biology 3301 or credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107) and Animal Science 3443.

4303 Evolution (3-0). A review of the history of evolutionary thought and discussion of the development of all living organisms from previously existing types under the control of evolutionary processes. Emphasis on the mechanisms of evolution and the different theories regarding the processes that have brought about evolutionary change.
Prerequisites: Credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107, 1480) and Biology 3301 or credit for one semester of introductory biology for majors (Biology 1306/1106, 1307/1107) and Animal Science 3443.

4315 Biogeography (3-0). A study of the distribution of plants and animals over the earth and of the principles that govern this distribution.
Prerequisites: Biology 1411 or 1413 or equivalent.

4381 Special Topics. Selected topics in biology. (May be repeated once for credit when the topic varies.)
Prerequisite: Junior standing.

4401 Ornithology (3-3). A study of the biology of birds, their anatomy, evolutionary history, diversity, ecology, behavior, and zoogeography. Laboratory exercises will emphasize the identification and natural history of Texas birds.
Prerequisite: Biology 1413 or equivalent.

4402 Mammalogy (3-3). A study of the biology of mammals, their anatomy, evolutionary history, diversity, ecology, behavior, and zoogeography. Laboratory exercises will emphasize the identification and natural history of Texas mammals.
Prerequisite: Biology 1413 or equivalent.

4403 Natural History of Bats (3-3). A study of the ecology and evolution of the order Chiroptera with emphasis on unique adaptations related to the life history strategies and echolocation of North American bats. Students will gain hands-on experience with the use of taxonomic keys and field techniques used in sampling and identifying bat species in natural habitats.
Prerequisite: Biology 1413 or consent of the instructor.

4404 Herpetology (3-3). A study of the amphibians and reptiles, their anatomy, evolutionary history, diversity, ecology, behavior, and zoogeography. Laboratory exercises will emphasize the identification and natural history of Texas amphibians and reptiles.
Prerequisite: Biology 1413 or equivalent.

4412 Biological Oceanography (3-3). A study of marine organisms and the environment in which they are found. Particular emphasis will be given to the Gulf of Mexico.
Prerequisite: Credit for one course in biology for majors (Biology 1306/1106, 1307/1107, 1411, 1413) or consent of instructor.

4421 Developmental Biology (3-3). A study of the molecular and genetic mechanisms regulating the development of animals. Specific topics include gametogenesis, embryogenesis, and tissue development. Laboratory explores the development of various invertebrate and vertebrate model organisms and emphasizes the application of techniques used with these model systems.
Prerequisites: Biology 3301, 3403.

4423 General Physiology (3-3). An advanced course in fundamentals of vertebrate physiology emphasizing function from the molecular to the organ system level. Laboratory exercises combine animal surgery, biochemical and molecular techniques, electronic instrumentation, and/or computer simulations of physiological principles.
Prerequisites: Must have completed Biology 1413, or Biology 1306/1106 and 1307/1107, or Biology 2323/2123 and 2324/2124, with a grade of 𠇋” or better.

4425 Bioinformatics (3-3). Introduction to methods for acquiring, analyzing, and employing biological sequence information. Topics will include- Theory and process of PCR, mass spectroscopy, and DNA microarrays. Algorithms for searching and clustering sequences. Applications of bioinformatic data to questions such as the geographical movement of Zika virus, horizontal gene transfer in bacterial viruses, and changes in human gene expression in response to disease and treatment. Students will access remote sequence databases (NCBI, EMBL-EBI) and analyze sequences with open source bioinformatics software running natively, in a Linux virtual machine, and on remote servers. Analyses will include protein structure prediction, phylogenetics using molecular data, and genome annotation. Students will annotate a novel viral genome and submit the completed annotation to NCBI. (Credit may not be earned for this course and Biology 5425.)

4435 Plant Taxonomy (3-3). Laboratory and field studies emphasize the use of a dichotomous key using flowering plants of the Concho Valley as topics of study, and recognition of the major families of flowering plants. Lecture emphasis is on current problems in plant taxonomy and systematics. (Credit may not be earned for this course and Range and Wildlife Management 4435.)

4441 Parasitology (3-3). A study of the anatomy, life cycles, ecology, diseases, diagnosis and treatment of protozoa, helminths, and arthropods parasitic in man. (Credit may not be earned for this course and Biology 5441.)
Prerequisites: Credit for two courses in biology for majors (Biology 1306/1106, 13071107, 1411, 1413), or (Biology 2323/2123 and 2324/2124).

4442 Arachnology (3-3). A study of the origin of the arachnids and their evolutionary relationships to other early arthropod groups. A survey of the recognized ordinal groups will be presented in both lecture and laboratory with respect to the existing literature on distribution, morphology, ecology, reproductive life cycles and their relationships to man.

4443 Invertebrate Zoology (3-3). A survey of major invertebrate phyla, with emphasis on the classes of Cnidarians, Annelids, Mollusks, Arthropods, and Echinoderms. Particular attention will be given to phylogenetic relationships and natural history.
Prerequisite: Biology 1413 or equivalent.

4450 Molecular Biology (3-4). A study of the synthesis, function, and regulation of biologically important macromolecules (DNA, RNA, and proteins). Laboratory exercises are designed to develop skills with standard techniques in molecular biology such as electrophoresis, PCR, recombinant DNA technology, DNA sequencing, and bioinformatics.
Prerequisites: 𠇌” or better in Biology 3403 or consent of instructor.

4451 Principles of Ecology (3-3). Examination of basic ecological concepts and principles of the ecosystem and biogeochemical cycles, with particular emphasis on the organization and energetics of populations at the species, interspecies, and community levels in aquatic and terrestrial environments.
Prerequisites: Credit for two semesters of biology for majors (Biology 1306/1106, 1307/1107, 1411, 1413), and Mathematics 1314 1342, or higher (e.g. Mathematics 1316, 2312, 2413, 2414) or consent of instructor.

4480 Introduction to Biometry (3-2). An introduction to the application of statistics to biological research. This course will include an introduction to probability, sampling theory, and hypothesis testing. Emphasis will be on common statistical techniques for biological research.
Prerequisites: Mathematics 1314 or equivalent. Mathematics 2312 or 3321 are recommended.


The Cerebral Cortex Creates Consciousness and Thinking

All animals have adapted to their environments by developing abilities that help them survive. Some animals have hard shells, others run extremely fast, and some have acute hearing. Human beings do not have any of these particular characteristics, but we do have one big advantage over other animals—we are very, very smart.

You might think that we should be able to determine the intelligence of an animal by looking at the ratio of the animal’s brain weight to the weight of its entire body. But this does not really work. The elephant’s brain is one thousandth of its weight, but the whale’s brain is only one ten-thousandth of its body weight. On the other hand, although the human brain is one 60th of its body weight, the mouse’s brain represents one fortieth of its body weight. Despite these comparisons, elephants do not seem 10 times smarter than whales, and humans definitely seem smarter than mice.

The key to the advanced intelligence of humans is not found in the size of our brains. What sets humans apart from other animals is our larger cerebral cortex —the outer bark-like layer of our brain that allows us to so successfully use language, acquire complex skills, create tools, and live in social groups (Gibson, 2002). In humans, the cerebral cortex is wrinkled and folded, rather than smooth as it is in most other animals. This creates a much greater surface area and size, and allows increased capacities for learning, remembering, and thinking. The folding of the cerebral cortex is referred to as corticalization.

Although the cortex is only about one tenth of an inch thick, it makes up more than 80% of the brain’s weight. The cortex contains about 20 billion nerve cells and 300 trillion synaptic connections (de Courten-Myers, 1999). Supporting all these neurons are billions more glial cells (glia) , cells that surround and link to the neurons, protecting them, providing them with nutrients, and absorbing unused neurotransmitters. The glia come in different forms and have different functions. For instance, the myelin sheath surrounding the axon of many neurons is a type of glial cell. The glia are essential partners of neurons, without which the neurons could not survive or function (Miller, 2005).

The cerebral cortex is divided into two hemispheres, and each hemisphere is divided into four lobes, each separated by folds known as fissures. If we look at the cortex starting at the front of the brain and moving over the top (see Figure 3.10 “The Two Hemispheres”), we see first the frontal lobe (behind the forehead), which is responsible primarily for thinking, planning, memory, and judgment. Following the frontal lobe is the parietal lobe , which extends from the middle to the back of the skull and which is responsible primarily for processing information about touch. Then comes the occipital lobe , at the very back of the skull, which processes visual information. Finally, in front of the occipital lobe (pretty much between the ears) is the temporal lobe , responsible primarily for hearing and language.

Figure 3.10 The Two Hemispheres

The brain is divided into two hemispheres (left and right), each of which has four lobes (temporal, frontal, occipital, and parietal). Furthermore, there are specific cortical areas that control different processes.


MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.


Watch the video: Notes for IB Biology Chapter (May 2022).


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