Survey of the Natural Sciences Study Guide for the DAT

Biology (continued)

Diversity of Life

Biologists organize all life on Earth into the three domains of Archaea, Bacteria, and Eukarya based on identifying characteristics that set them apart. Domains are broken down into six kingdoms: Archaebacteria, Eubacteria, Protista, Fungi, Plantae, and Animalia. From there kingdoms are divided into phyla, phyla into divisions, divisions into classes, classes into orders, orders into families, families into genera, and genera into species. For their scientific names, organisms are identified by their genus and species name.

Viruses

Viruses were not mentioned in the organization of living things because viruses are nonliving organisms. Viruses are not able to carry on any processes outside of a host. Their life cycles are either lytic or lysogenic, and they can contain DNA or RNA enclosed by a protein coat similar to a cell membrane in our cells.

Archaebacteria

The single-celled archaebacteria are prokaryotic and closely related to eubacteria, but because they are not a type of bacteria, they have their own kingdom classification (Archaebacteria). Archaea cell membranes are uniquely made of glycerol-ether lipids, and cells contain some enzymes unique to archaea. This is because some archaea, called extremophiles, evolved to survive in extreme environments where other cells are unable to thrive.

Eubacteria

Like archaea, eubacteria are prokaryotic cells. These cells contain a loop of DNA and are often encapsulated by a cell wall. These single-celled organisms are bacteria, unlike archaea, and are classified by their morphological shape (cocci, bacilli, spirilla, duplexes, clusters, and chains).

Fungi

Similar in structure to plant cells, fungi cell walls contain chitin. Fungi are heterotrophic and often saprophytic, meaning they feed on dead organisms by absorbing nutrients from the surrounding environment. They reproduce asexually via sporulation and include mushrooms, yeast, and lichens.

Protista

Kingdom Protista consists of phyla protozoa, algae, and slime molds, which are all eukaryotic organisms. Protozoa are motile via various cellular extensions like pseudopods and cilia. Algae, such as phytoplankton and kelp, can perform photosynthesis. Lastly, slime molds are categorized as Protista because they exhibit animal and plant-like cellular activity (they were once classified as Fungi). The unique aspects of slime molds include sporulation reproduction and their structure having multiple nuclei (coenocytic) in a mass of protoplasm.

Plantae

Kingdom Plantae is set apart from others due to their ability to perform photosynthesis and synthesize their own food from their environment using a special organelle called a chloroplast. Because of this, they are classified as autotrophs. Other unique structures of these organisms include vascular tissues for water transport, cuticles to prevent water loss, and stomata, which function as a respiratory system.

Bryophytes are a phylum of plantae that must live in moist environments, as they do not have as developed of a water transport system. Mosses and liverworts are examples of bryophytes.

Tracheophytes are another phylum. These have well-developed vascular systems, radial symmetry, and deep root anchoring structures.

Both phyla Pteridophyta and Lycophyta are non-seed-bearing Plantae. Pteridophyta, including ferns, have large root and vascular systems and reproduce via spores. Lycophyta also have root systems. Additionally, these nonwoody plants, such as club mosses, have microphyll leaves.

Angiosperms is a large phylum containing a considerable diversity of organisms. The males use the anther of the stamen to make microspores, while the female pistils make megaspores. Fertilization occurs and the embryo eventually develops into a covered seed, which becomes a fruit. Angiosperms are further broken down into dicotyledons and monocotyledons. Dicotyledons have netted veins and two cotyledons in the seed, and they lower in multiples of four or five. Monocotyledons have parallel veins, single cotyledons, and nonwoody characteristics, and they flower in multiples of three.

Gymnosperms have exposed seeds, are woody, and include conifers, cycads, gnetophytes, and ginkgo.

Animalia

Kingdom Animalia are typically heterotrophic, bilaterally symmetric, and motile with many specialized body systems. There are over 30 phyla within this kingdom. Porifera, like sea sponges, differ in that they are immotile and lowly specialized. Cnidaria have ectoderm and endoderm, radial symmetry, tentacles, stinging cells, and nerve nets. Platyhelminthes, like flatworms, and Nematoda, like roundworms, contain ectoderm and endoderm like cnidaria as well as a third layer called mesoderm. They don’t have circulatory systems and have a primitive nervous system.

Segmented worms, which fall in the Annelida phylum, contain well-developed systems, including digestive, circulatory, nervous, and excretory. Mollusca are differentiated by their soft bodies, exoskeletons, and mantels. As they exist in water, they have gills along with chambered hearts, blood sinuses, and paired ventral nerve cords. Arthropoda also have exoskeletons and blood sinuses and include insects, arachnids, and crustaceans.

Echinodermata are radially symmetrical and can regenerate parts that are damaged or lost. Chordata are distinct in that they have a notochord during development but are not considered vertebrates.

Vertebrata have a backbone and skull instead of a notochord and contain many different classes with individualized characteristics setting them apart. Agnatha include jawless fish, which actually keep their notochord, setting them apart from all other vertebrates.

Chondrichthyes, like sharks, keep a reduced version of a notochord and the remainder of their vertebrates are made of cartilage. Osteichthyes are also called bony fish. These animals have scales and bony skeletons with no notochord.

Amphibia start their life cycles in the water with gills and a tail. They progress to be land-dwelling as they age, developing lungs, legs, and a three-chambered heart while losing the tail and scales.

Reptilia always live on land and develop lungs, legs, scales, and a three-chambered heart. They reproduce via internal fertilization and lay eggs.

Aves includes birds that lay eggs, similarly to reptilia, but they differ in that they are warm-blooded.

Mammalia are also warm-blooded like aves, but they differ in that they feed their young with their own milk. This class is further broken down into Monotremata, Marsupialia, and Placentalia, which differ in the way they produce their offspring. Humans are a part of the later group.

Integrated Relationships

In any given ecosystem, you may notice all kingdoms represented. Their interactions can be classified as parasitism, commensalism, or mutualism based on the outcomes of those interactions. In parasitism, one organism benefits while the other organism is harmed. In commensalism, one organism benefits and the other is unharmed but receives no benefits. Lastly, mutualism is when both organisms involved in the relationship benefit.

Structure and Function of Systems

There are many specialized systems that make up the body that are designed to maintain basic bodily functions and homeostasis. These individual systems work together to respond to external and internal stimuli to minimize impact on the body itself. Each system has individual components that are designed to perform the jobs that the respective system is responsible for, such as lungs that are specialized within the respiratory system for breathing.

Integumentary

The integumentary system is the way the body guards itself from outside threats like pathogens via physical barriers like skin, hair, nails, feathers, fur, hooves, husks, and shells, to name a few. The skin is a principle player in the integumentary system as the microbiome, pH, and sweat production can help an animal respond to its surroundings. The epidermis and dermis compose the skin and are interconnected via a basement membrane. Within these layers are hair cells, sweat glands, mucous glands, and enzymes that help to detect and respond to stimuli as well as maintain a livable environment internally for the animal.

Skeletal

The skeletal system exists to protect internal organs using cartilage and bone. Chondrocytes are specialized cells that produce cartilage, which is more flexible than bone but still provides a degree of protection. Compact bone composes much of the skeletal system and provides much of its strength while spongy bone is found at the end of long bones and in marrow cavities. Osteoblasts make bone via endochondral ossification, through which cartilage is transformed into bone, and intramembranous ossification, though which undifferentiated connective tissues are ossified to form bone. Osteocytes break down bone.

Muscular

Smooth muscle is muscle that controls involuntary actions of the autonomic nervous system.

Skeletal muscle of the somatic nervous system is composed of myofibrils and sarcomeres. The sarcomeres are composed of thick myosin filaments and thin actin filaments. The sarcomere structure is depicted in the graphic below. During contraction of a muscle, the A band remains the same size while the H zone and I band shrink.

An action potential from a neuron stimulates the sarcolemma and T tubule system of the muscle cell that releases stores of intracellular calcium from the sarcoplasmic reticulum. The calcium binds the troponin C protein to the actin filaments, which causes exposure of myosin binding sites. This enables actin and myosin to interact and a contraction to occur. Calcium is pumped back into the sarcoplasmic reticulum and the muscle relaxes.

Circulatory

The role of the circulatory system is to successfully and efficiently pump blood throughout the body and to maintain a certain oxygenation level of said blood. Therefore, the circulatory and respiratory systems work very closely with one another.

It is important to understand the structure of the heart. Deoxygenated blood flows through the respective vena cava into the right atrium, through the tricuspid valve, into the right ventricle, and out of the heart via the pulmonary arteries by way of the pulmonary valve. From there the blood gets oxygenated by the lungs and flows back into the heart via the pulmonary veins into the left atrium, through the mitral valve, into the left ventricle, and out into the body via the aorta via the aortic valve. Arteries move the blood away from the heart, and veins move the blood toward the heart.

Retrieved from: https://openstax.org/books/biology-2e/pages/40-3-mammalian-heart-and-blood-vessels

The layers of tissue that make up the heart include the inner layer called the endocardium, which is attached to the muscular portion called the myocardium. This layer is covered by the epicardium and the pericardium. The heart itself receives blood via the coronary arteries.

Systole describes when the heart is contracting, and diastole describes when the heart is relaxing. During this period of relaxation, the heart is filled with newly oxygenated blood, which will be pumped to the body in the next period of contraction. The rhythm of the heart is set by the sinoatrial (SA) node.

Blood is made up of two components, cellular and non-cellular. Plasma is the portion devoid of cells and offers the mixture of blood many ions, proteins, and gases. The cellular portion is composed of leukocytes (or white blood cells), platelets, and erythrocytes (or red blood cells). Leukocytes play a role in immunity, and platelets are involved in clot formation. Erythrocytes are involved in the oxygenation of blood.

Lymphatic/Immune

The immune system is composed of both innate and adaptive immunity. Innate immunity includes the skin of the integumentary system, as previously mentioned, and actions like inflammatory responses and other physiological responses to elements. Some important components of the innate portion of the immune system are summarized in the table below:

Cell type	Characteristics	Location
Mast cell	Dilates blood vessels and induces inflammation through release of histamines and heparin. Recruits macrophages and neutrophils. Involved in wound healing and defense against pathogens but can also be responsible for allergic reactions.	Connective tissues, mucous membranes
Macrophage	Phagocytic cell that consumes foreign pathogens and cancer cells. Stimulates response of other immune cells.	Migrates from blood vessels into tissues.
Natural killer cell	Kills tumor cells and virus-infected cells.	Circulates in blood and migrates into tissues.
Dendritic cell	Presents antigens on its surface, thereby triggering adaptive immunity.	Present in epithelial tissue, including skin, lung and tissues of the digestive tract. Migrates to lymph nodes upon activation.
Monocyte	Differentiates into macrophages and dendritic cells in response to inflammation.	Stored in spleen, moves through blood vessels to infected tissues.
Neutrophil	First responders at the site of infection or trauma, this abundant phagocytic cell represents 50-60 percent of all leukocytes. Releases toxins that kill or inhibit bacteria and fungi and recruits other immune cells to the site of infection.	Migrates from blood vessels into tissues.
Basophil	Responsible for defense against parasites. Releases histamines that cause inflammation and may be responsible for allergic reactions.	Circulates in blood and migrates to tissues.
Eosinophil	Releases toxins that kill bacteria and parasites but also causes tissue damage.	Circulates in blood and migrates to tissues.

Adapted from: https://openstax.org/books/biology-2e/pages/42-1-innate-immune-response

Granulocytes include immune response cells that travel to the area of injury to get rid of antigenic material. These include neutrophils, eosinophils, basophils, and mast cells, whose roles are discussed in the table above.

Monocytes are immune response cells that develop into either macrophages or dendritic cells.

Adaptive immunity is when the immune system learns how to respond to a given pathogen through various means and is better able to fight against the antigen(s). T cells are reactive to a given antigen. When the organism comes into contact with the antigen, antigen-presenting cells will display a major histocompatibility complex (MHC), which will then recruit appropriate T cells to the area to perform their jobs.

MHC I complexes recruit CD8+ or cytotoxic T cells, which kill the cells that are infected with the antigens like viruses or tumor cells. MHC II complexes recruit T helper cells. T helper cells release substances called cytokines, which signal to the rest of the body that there is an antigen present and stimulate immune responses to defeat that antigen. Natural killer T cells detect intracellular infection by detecting the expression or lack thereof of MHC complexes. Memory T cells allow for more speedy reaction to the antigen in the future, since the organism has already had an interaction with said antigen.

B cells are responsible for creating antibodies, which specifically bind to antigens to mount an immune response to them.

The lymphatic system is composed of lymph nodes and the spleen, which collects, filters, and detects antigens to alert the immune system when needed.

Digestive

The digestive tract begins at the oral cavity and follows a path through the pharynx, esophagus, stomach, small intestine, and large intestine before exiting at the anus. Saliva provides amylase, which starts to break down food chemically in addition to the mechanical digestion provided by mastication. From there, food is swallowed and passed through the esophagus via muscular contractions called peristalsis. Once the bolus enters the stomach, specialized cells produce acidic enzymes to further break down the food. The cell types are summarized in the table below:

\[\begin{array}{|l|l|} \hline \textbf{Mucous Cells} & \begin{array}{l} \cdot \text{ Found in gastric pits} \\ \cdot \text{ Secrete mucus to protect the stomach from acidic environment} \end{array} \\ \hline \textbf{Chief Cells} & \begin{array}{l} \cdot \text{ Found in gastric glands} \\ \cdot \text{ Produce pepsinogen, which becomes pepsin} \end{array} \\ \hline \textbf{Parietal Cells} & \begin{array}{l} \cdot \text{ Found in gastric glands} \\ \cdot \text{ Synthesizes HCl} \\ \cdot \text{ Produces intrinsic factor, promotes absorption of Vitamin B12} \end{array} \\ \hline \end{array}\]

The food bolus leaves the stomach and enters the small intestine where it is chemically digested further and its nutrients are absorbed through villi. The liver produces a substance called bile, which emulsifies fats so that they can be broken down.

The process of digestion is controlled hormonally through the hormones summarized in the table below:

\[\begin{array}{|l|l|} \hline \textbf{Gastrin} & \begin{array}{l} \cdot \text{ Produced by the G cells of the duodenum of the small intestine} \\ \cdot \text{ Tells parietal cells to make HCl} \\ \cdot \text{ Promotes histamine and pepsinogen release} \end{array} \\ \hline \textbf{Intrinsic Factor} & \begin{array}{l} \cdot \text{ Produced by the parietal cells of the stomach} \\ \cdot \text{ Stimulates absorption of B12 by the intestine} \end{array} \\ \hline \textbf{Cholecystokinin (CCK)} & \begin{array}{l} \cdot \text{ Produced by the I cells of the duodenum and jejunum} \\ \cdot \text{ Stimulates pancreatic enzyme, somatostatin, and gallbladder contraction} \\ \cdot \text{ Acts as hunger suppressant} \end{array} \\ \hline \textbf{Secretin} & \begin{array}{l} \cdot \text{ Produced by S cells of the upper intestine} \\ \cdot \text{ Encourages bicarbonate, blocks gastric emptying and acid production} \end{array} \\ \hline \textbf{Ghrelin} & \begin{array}{l} \cdot \text{ Increases appetite} \end{array} \\ \hline \textbf{Leptin} & \begin{array}{l} \cdot \text{ Produced in fat cells} \\ \cdot \text{ Opposes ghrelin} \\ \cdot \text{ Reduces appetite} \end{array} \\ \hline \end{array}\]

Respiratory

Air passes through the nose or mouth and follows a path of the pharynx, larynx, trachea, bronchi, and bronchioles, before finally arriving at the alveoli of the lungs. Lungs maintain their shape and avoid collapse due in part to a protein called surfactant. The respiratory centers that control breathing are located in the medulla oblongata. The respiratory center receives input from chemoreceptors, which measure the levels of carbon dioxide in the bloodstream.

Capillaries surround the alveoli and carry oxygen-poor blood to the lungs. Oxygen will flow from areas of higher partial pressure to areas of lower partial pressure and oxygenate the blood at the capillaries.

The maximum volume of air lungs can hold is called total lung capacity, while the volume of air inhaled or exhaled during resting breath is called tidal volume. Inspiratory reserve volume is the difference between inspiratory capacity and tidal volume. Expiratory reserve volume is the vital capacity of the lungs less the inspiratory reserve volume and the tidal volume. Vital capacity is the volume of air during maximum inhalation and maximum exhalation. The residual volume is the volume of air that is left in the lungs to keep the alveoli from collapse. All of this is summarized in the figure below:

Retrieved from: https://openstax.org/books/biology-2e/pages/39-2-gas-exchange-across-respiratory-surfaces

Urinary

The body’s salt-to-water balance is maintained by the kidneys. The kidney is organized into nephron functional units consisting of a glomerulus contained in a Bowman’s capsule. Fluid then passes through the proximal convoluted tubule, the loop of Henle (first descending, then ascending), the distal convoluted tubule, and, finally, the collecting duct, where various ions pass into and out of the fluid passing through the kidney. The passage of ions and fluids are summarized in the table below:

\[\begin{array}{|l|l|} \hline \textbf{Glomerulus} & \text{Filters small solutes from the blood} \\ \hline \textbf{Proximal convoluted tubule} & \begin{array}{l} \text{Reabsorbs ions, water, and nutrients} \\ \text{Removes toxins and adjusts filtrate pH} \end{array} \\ \hline \textbf{Descending loop of Henle} & \begin{array}{l} \text{Aquaporins allow water to pass from the} \\ \text{filtrate into the interstitial fluid} \end{array} \\ \hline \textbf{Ascending loop of Henle} & \begin{array}{l} \text{Reabsorbs Na+ and Cl- from the filtrate into} \\ \text{the interstitial fluid} \end{array} \\ \hline \textbf{Distal tubule} & \begin{array}{l} \text{Selectively secretes and absorbs different} \\ \text{ions to maintain blood pH and electrolyte balance} \end{array} \\ \hline \textbf{Collecting duct} & \text{Reabsorbs solutes and water from the filtrate} \\ \hline \end{array}\]

The filtrate flows into the ureter where it is called urine. Urine is formed through filtration, secretion, and reabsorption.

Nervous/Sensory

There are two parts to the nervous system, the central nervous system (CNS) and the peripheral nervous system (PNS). Neurons are the main specialized cells that compose the nervous system, but there are also support cells called neuroglia or glial cells.

Neurons are composed of dendrites, which receive information and transport it to the soma (cell body). The information is then passed down the axon of the neuron all the way to the synapse, where the information is turned into a signal of neurotransmitters to pass along the message to neighboring neurons and stimulate a response in the body. Neurons are insulated by a substance called myelin, which allows for a signal to more successfully and quickly be sent. The nodes of Ranvier are the gaps in myelin and contribute to saltatory conduction.

Neurons operate with an all-or-nothing response. This means that an action potential is either triggered or it isn’t, and the size of the signal does not change the strength of the action potential. Once a threshold potential is reached, sodium (Na+) channels open, allowing sodium into the cell, and the cell depolarizes. When the cell reaches a peak of around +35 millivolts (mV), voltage-gated potassium (K+) channels open to repolarize the cell. In the process of repolarizing the cell and getting the cell back to its resting potential, the cell goes through a refractory period when the cell is hyperpolarized. All of this is summarized in the figure below:

Retrieved from: https://openstax.org/books/biology-2e/pages/35-2-how-neurons-communicate

There are many different types of glial cells, including astrocytes, satellite glia, microglia, oligodendrocytes, Schwann cells, and ependymal cells. Their functions are summarized in the table below:

astrocyte	found in CNS, provide nutrients and support, regulate chemicals in extracellular fluid (ECF), form blood-brain barrier
satellite glia	provide nutrients and support in the PNS
microglia	break down dead cells and protect from pathogens
oligodendrocytes	form myelin sheaths in the CNS
schwann cells	form myelin sheaths in the PNS
ependymal cells	produce cerebrospinal fluid (CSF) in the spinal cord

The brain is divided into forebrain, midbrain, and hindbrain. The forebrain is largely composed of the cerebral cortex but also contains the olfactory bulb, thalamus, and hypothalamus. The hypothalamus is the control center for various functions like hunger, thirst, water balance, and more. The midbrain is centrally located and has roles in relaying visual and auditory information as well as in motor control. The hindbrain contains the cerebellum, pons, medulla, and brainstem.

The spinal cord is a way for the body to conduct signals to the brain from the body. Reflexes can sometimes occur on their own at the spinal cord level. Sensory information enters the spinal cord via the dorsal horn, while motor information leaves the spinal cord via the ventral horn.

The peripheral nervous system is made up of two components: somatic nervous system and autonomic nervous system. The somatic nervous system is responsible for voluntary movement in the form of reflexes and skeletal muscle movement. The autonomic nervous system controls involuntary processes that help keep the body at homeostasis without conscious effort.

The autonomic nervous system is further broken down into sympathetic nervous system and parasympathetic nervous system. The sympathetic nervous system primarily uses the neurotransmitter norepinephrine to prepare the body for fight or flight responses like increasing blood flow and dilating bronchioles to allow for improved breathing efficiency. The parasympathetic nervous system primarily uses the neurotransmitter acetylcholine to conserve energy during periods of rest and digestion by lowering heart rate and increasing gut function and motility. These two systems complement one another to regulate bodily function and keep the body at homeostasis, which is illustrated in the figure below:

Retrieved from: https://openstax.org/books/biology-2e/pages/35-4-the-peripheral-nervous-system

Endocrine

The endocrine system utilizes hormones to regulate bodily functions. There is a negative feedback loop where, once the desired result has occurred, the hormone is instructed by the body to cease production.

Endocrine Glands and Their Hormones
Endocrine Gland	Hormones and Effects
Hypothalamus	TRH: Stimulates thyroid hormones release GnRH: Stimulates FSH and LH release GHRH: Stimulates GH release CRH: Stimulates ACTH release Somatostatin: Inhibits TSH and GH Dopamine: Increases prolactin production Vasopressin: Increases water reabsorption (kidneys)
Anterior Pituitary	GH: Promotes growth, protein synthesis Prolactin: Stimulates milk production TSH: Stimulates thyroid hormone release ACTH: Stimulates adrenal cortex FSH: Stimulates gamete production LH: Stimulates ovulation, androgen production MSH: Increases melanin production
Posterior Pituitary	ADH: Water reabsorption (kidneys) Oxytocin: Uterine contractions, milk ejection
Thyroid	Thyroxine, Triiodothyronine: Stimulate metabolism, growth Calcitonin: Reduces blood calcium levels
Parathyroid	PTH: Increases blood calcium levels
Adrenal Cortex	Aldosterone: Increases Na+, K+ secretion Cortisol: Increases glucose, anti-inflammatory
Adrenal Medulla	Epinephrine, Norepinephrine: Flight or fight response
Pancreas	Insulin: Reduces blood glucose Glucagon: Increases blood glucose
Pineal Gland	Melatonin: Regulates rhythms, protects CNS
Testes	Androgens: Sperm production, secondary characteristics
Ovaries	Estrogen: Uterine lining growth, fat distribution Progestins: Maintain uterine lining growth

Reproductive

Spermatogenesis, or the production of sperm, occurs in the testes. The maturing sperm cells progress to the epididymis then out through the vas deferens and urethra. As aforementioned in the endocrine system portion, FSH is produced to mature the male sex organs and characteristics. This hormone acts on Sertoli cells located in the seminiferous tubules of the testes to promote sperm development and production. LH, another hormone of the endocrine system, acts on Leydig cells in the testes to make testosterone.

Ovaries contain many follicles that each protect an ovum. During ovulation, an ovum is released into the abdominal cavity where it eventually travels through the fallopian tube into the uterus. If the ovum is fertilized here, this will be the site of future development of the fetus. If the ovum is not fertilized, it is lost through the menstrual cycle. LH and FSH regulate the release of estrogens and progestins by the ovaries.

Integrated Relationships

It is important to understand that the kidney and renal and urinary system can impact the circulatory system and respiratory system as well as many others to remove wastes and maintain the body at an appropriate pH level. A similar interaction of systems is on display when you consider the hormones of the endocrine system and their huge impact on the function and development of many other systems and parts of the body.