BIOL 1111 Course Overview PDF

Overview of BIOL 1111 ===================== **Introductory Notes** ---------------------- BIOL 1111 starts at the basic parts that make up a human being (from the *atom*, not the *cell*) so expect a lot of basic biochemistry. The impact of biological science will be discussed in the course: vaccines, treatments, diseases, etc. The course goes from A-to-B from elementary biochemistry to the immune system: ***Intro to Biology (Chap I)*** ***Chemistry and Molecules of Life (II-III)*** ***Cell Function and Structure (IV-V)*** ***Digestion and Nutrition in Animals (XXVI)*** ***Animal Structure and Function (XXV)*** ***Circulation (XXVIII)*** ***Respiration*** ***Microbiology (XVII)*** ***Reproduction (XXVIII)*** ***Immune System (XXXIV)*** all discussed from September 2 to November 25, covering Chapters 1-34 of the textbook. Finals will take place anywhere from Dec 4-16, so tell everyone to ***sod off*** for this period of time, no you're not available, no you can't do anything, no you can't go on any multi-day side-quests, ***lock in.*** There will be four quizzes -- each of them announced one week in advance and the lowest one will be dropped. Conway's advice -- Don't use your grace-quiz on the first one. Or, and this is a better option, ***knock all these quizzes so far out of the park that you won't need it.*** Don't be a gonk -- show up to all the lectures. There will be random in-class assignments worth 5% of your grade. Conway will eyeball you if you're on your phone and stop the lecture until you realize that the entire class has gone quiet, and Conway is evil eyeing you. Don't be that guy. This should go without saying -- don't cheat. Automatic zero. The course outline says to not record the lectures, but Conway doesn't care, so if you need to, do it. You paid to be here, so be here. Don't start playing Civ in the background or posting while class is going on. There will be SFAT (Study for a Test) markers throughout this document to give an overview of everything worth knowing for any upcoming test or examination. Are we good to go? Good. Chapter 1 -- Introduction to Biology ==================================== The cell is often described at the basic unit of life. Anything below this (organelles, etc.) is not congruent with the ***seven characteristics of life-forms** --* more elaboration on this later. A basic understanding of biology is probably necessary for an informed understanding of many issues. Biology Myths ------------- - Drink 64 ounces (8 8oz glasses of water every day)? ***False***. This comes from a 1949 footnote in an American food guide. The guide refers to ***total water content*** consumed per day, including foods with water in them. - We use only 10% of our brains? ***False***. Evolution does not waste space like that. - Right-handed people live on average 10 years longer than left-handed people? ***False.*** It's context specific. Working around heavy machinery dependent on right-handedness may skew this towards -10 years. - Your brain uses 20% of the oxygen in your bloodstream? ***True***. Your brain is *extremely* metabolically active. - Hair and fingernails continue to grow after death? ***False.*** Your skin dehydrates and shrinks a little bit after you die, which gives the illusion that your hair and fingernails are longer. - Reading in dim light ruins your eyesight? ***False***. Maybe it gives you a headache, but it will not change your acuity. - It takes more muscles to frown than to smile? ***False***. You use 1-2 more muscles to smile than to frown. - Eating turkey makes people drowsy? Turkey has a high concentration of amino acid called *tryptophan*. Melatonin, the sleepy hormone, is a derivative of tryptophan, so your body converts it to melatonin, which makes you sleepy.\....which is what I would say if it were true, but it's ***false***. It's just the gargantuan concentration of food people eat on thanksgiving. - The average person farts 14 times a day? ***True.*** - Humans evolved from chimpanzees? ***False***. We have a common ancestor, but chimps are not our direct ancestors. - Gum takes 7 years to digest? ***False***. - Sharks don't get cancer? ***False.*** They very rarely get cancer, but they do. - Waking sleepwalkers can harm them? ***False.*** - Antibiotics do not cure the common cold? ***True***. Antibiotics cannot kill viruses, which cause the common cold. - Vitamin C supplements can prevent the common cold/flu? ***False.*** No impact on your immunobiology. - You can get warts from touching a toad? ***False***. HPV causes warts, not toads. So, pet your local toads. - The human body is estimated to have 60,000 miles of blood vessels? ***True***. - Sneezes exceed over 100mph? ***False**.* It's like, 20mph. 100mph, you die. - The redhead gene will become extinct within the next 100 years? ***False***. It's just a recessive gene. It might present in low numbers, but it'll always be here. - The brain itself cannot feel pain? ***True***. No touch, and no pain. If you feel a migraine, it's your blood vessels, which ***can*** feel pain. So, what even ***is*** Science, anyway? --------------------------------------- Science is the process of using observation and experimentation to draw evidence-based conclusions. What characteristics and processes distinguish living things from nonliving things? ----------------------------------------------------------------------------------- ***SFAT*** - All living things are made up of one or more cells - Life is recognized by what living things are able to do - There are ***Seven Characteristics of Life-forms*** that are commonly agreed upon. - ***Order***: The highly ordered structure that typifies life. - ***Reproduction***: Organisms reproduce their own kind. - ***Growth and Development***: Organisms grow and develop, with that process controlled by inherited DNA. - ***Energy Processing***: Organisms process energy and use it to do things. - ***Response to Environmental Stimuli***: Organisms respond to environmental stimuli. - ***Regulation***: Every organism controls its internal environment within limits that sustain life. - ***Evolutionary Adaptation***: Adaptations evolve over many generations as individuals with traits suitable for their environment pass their traits onto offspring. Levels of Organization concerning Biology ----------------------------------------- Life is organized into several structural levels forming hierarchies. Life can be studied from the smallest atoms to the entire living planet. The most common biological organization is this: - **Biosphere:** The biosphere refers to all of the environments on a planet that support life, i.e., the Earth. - **Ecosystem:** An ecosystem represents all the organisms living in a particular area where the physical components of the area and the organisms interact, for example, the ocean, a cave, etc. - **Community:** A community is a certain array of all the living organisms in a particular area, like, for example, a certain forest, or a certain area of the ocean floor. - **Population:** A population is all of the individuals of a species living in a particular area, for example, a subset of sea sponges living in a particular area in the Atlantic Ocean. Key terms concerning biology: - An **organism is an individual living thing**, like a specific human being. - An **organ system** is comprised of several organs that cooperate to achieve a certain function. - An **organ** is a structure composed of several living tissues that provide a specific function for an organism. - **Tissues** are a group of similar cells that perform a specific function. - **Cells** are the fundamental unit of life. Nothing is truly "living" below this. - An **organelle** is a membrane-bound structure that performs a certain function for a cell. - A **molecule** is a cluster of small chemical units called atoms held together by chemical bonds. - An **atom** is the most basic unit of matter. Emergent Properties ------------------- New properties arise as cells form tissues form organs form organ systems.... You get the idea. Like an SDRAM cell is capable of comprehending 1 or 0, a neuron is capable of comprehending a synapse or a lack thereof. 64 SDRAM cells are capable of comprehending a single data word, and a cluster of neurons are capable of comprehending a basic memory. An entire DRAM chip, comprised of billions of DRAM cells, is able to comprehend complex data structures, asset storage, programmed instructions, the same way the human brain, comprised of billions of neurons, is able to comprehend mathematics, images, memories, and complex multilayer instructions. Evolution --------- The theory of evolution by natural selection has revolutionized biology. - A **theory** provides a framework with great explanatory power.\ It's only really graduated to a theory because it has *stood the test of time.* Cells as the Fundamental Unit of Life ------------------------------------- The cell theory states: - All living things consist of cells - All cells are derived from preexisting cells - The ability of cells to divide and form new cells is the basis for all reproduction and development. All cells are enclosed by a membrane that regulates the passage of materials between the cell and its surroundings. All cells use DNA (Deoxyribonucleic Acid) as their genetic information. ***The unifying feature of life is based on heritable information, in the form of DNA.*** All living cells have DNA as their genetic material that are arranged into large genetic structures called chromosomes. We, human beings, have about 20,000 genes, and 46 chromosomes arranged into 23 pairs. Genes are segments of DNA encoded on chromosomes and act as the primary inheritance modus operandi. Diversity as the Hallmark of Life --------------------------------- There are roughly 1.8 million species identified and named to date, and thousands more are identified each year. Organizing the Diversity of Life -------------------------------- ***Taxonomy*** is the field of naming and classification of species, organizing them into a system of broader groups. Taxonomic groups follow like: - Domain: There are three domains of life, ***Bacteria, Eukarya, and Archaea***. We have eukaryotic cells (cells defined by higher-order structures like organelles and nuclei), which means we belong to Eukarya. Bacteria and Archaea are typically alike, except for the fact that Archaea typically live in the most extreme environments. - Kingdom, which includes ***Animalia, Plantae, Fungi, and Protists***. Humans are animals, so we belong to Animalia. - Phylum, of which there are over a hundred, including Arthropoda, Brachiopoda, Chordata, Porifera all under Animalia. Our phylum is ***Chordata***, as we have a dorsal nerve cord in the presence of our spinal cord. - Class, of which there are over 100 in the Animal Kingdom alone. We belong to class ***Mammalia***, as our babies are born alive. - Order, of which we are ***Primates***. - Family, of which we belong to the family of ***Hominids***. - Genus, of which we belong to ***Homo***. - Species is the most exclusive taxonomic group. We are ***Homo sapiens*** (the extra ***sapiens*** was dropped a while ago) , meaning, *wise man*. The Theory of Natural Selection ------------------------------- The theory of natural selection comes from Charles Darwin's *Origin of the Species by Means of Natural Selection* (1859). Darwin derived this theory from his voyage to the Galapagos Islands, finding finches that were mostly the same from island-to-island, with minor differences that made them able to adapt to the environment of every island. Darwin's theory made two main points: - These species of finches showed evidence of "descent with modification" from common ancestors. - Natural selection is the *mechanism* behind evolution. Darwin's theory explained the duality of unity and diversity. - Similar traits among organisms are explained by descent from common ancestors. - Differences among organisms are explained by their acclimation to their individual environments. Natural selection was inferred by connecting two observations: 1. Individuals in a population vary in their traits, of which many are passed from parent to offspring. 2. A population can produce more offspring than an environment can support. Therefore, individuals with heritable traits best suited to the environment are more likely to survive and reproduce than less well-suited individuals. As a result of this, an increasing proportion of individuals will have the advantageous traits, and the result will be evolutionary adaptation. The Process of Science ---------------------- Scientists use two main approaches to learn about the natural world around them: - **Discovery Science** involves describing some aspect of the world and using *inductive reasoning* to draw a general conclusion. - **Hypothesis-Driven Science** utilizes the ***Scientific Method*** and *deductive* *reasoning*. ### Discovery Science Discovery Science derives general principles from a large number of specific observations.\ After 200 years of cells discovered in all biological specimens observed, scientists concluded that all living organisms are made of cells. ### Hypothesis-Driven Science and the Scientific Method Hypothesis-Driven Science starts from a general hypothesis based on observations which is tested to determine if it can be applied to specific observations. - The scientific method starts with an **Observation** where previous experiments or results from others dictate what the scientist has seen. - From this, derive **Questions** about unclear aspects of observations. - Next, form a **Hypothesis**, which is an explanation of phenomena in the observation which is phrased in a ***testable*** and ***falsifiable*** (adjective: Able to be proven false) way. - Use this hypothesis to make a **Prediction** (for example, if (***hypothesis***) then ***prediction*** is ***true***) - Then, run **Tests** to determine whether our predictions are supported. - Ideally, you would use control tests (with a static variable to give a baseline) and then ***experimental tests*** (with a dynamic variable to test your hypothesis to prove or disprove your hypothesis. ### Null and Alternative Hypotheses Ideally, when forming a hypothesis, you want to form two hypotheses -- a **[null hypothesis]** and an **[alternative hypothesis.]** Suppose you wanted to test whether soaking a loaf of bread in water before leaving it in the dark leads to accelerated mold growth. Your **[null]** hypothesis would suppose that soaking a loaf of bread in water has no effect on mold growth. Your **[alternative]** hypothesis is that soaking a loaf of bread in water accelerates mold growth. Your research focus should be to ***disprove*** the null hypothesis before moving on to accept the alternative hypothesis as truth. Effectively, you're aggressively playing devil's advocate until it isn't feasible anymore. ### More on Testing When testing, you want to make sure that there is only one-variable-difference between your control and experimental groups to make sure that your results aren't skewed by any other variable. If you were to, say, test the effect of a pill on an athlete's performance, you'd want to make sure the athletic performance of the athletes isn't skewed by any other variable except for "Has the athlete taken the performance pill? Yes/No". Recall from PSYC 1115 -- Your results ought to be replicable and double-blind tested. Ideally, you'd tell both groups that they received the performance pill and give a pill to them, except one group only gets a sugar pill while the other group gets the pill that you're testing. Remember that tests ***cannot prove with absolute certainty*** any hypothesis. We can only run close to absolute certainty like an asymptote, by testing and testing and testing and testing to descend towards truth like a Newtonian gradient descent. ### Theories A scientific theory is: - Broader scoped than a hypothesis - General, and can lead to new testable hypotheses - Supported by a large body of evidence in comparison to a hypothesis. ### Applications of Hypotheses When we apply hypotheses in real life, we use ***deductive reasoning*** -- the type of reasoning where we work systematically through the list of possible issues when trying to solve a problem where the root problem may not be apparent. Suppose your flashlight is broken. You work through the potential problems one-by one: - Perhaps the batteries are dead? - **You replace the batteries with ones that you know aren't dead. You turn the flashlight on. No response.** - Perhaps the bulb is burnt out? - **You unscrew the front of the flashlight. You replace the bulb. You turn it on. The flashlight turns on.** - Maybe the wiring inside is corroded? - Etc., etc., etc. What that process is known as is ***deductive reasoning*** -- working from the lowest-hanging-fruit of problems up to the highest-cost-fruit to find the problem. You do this all the time, ***visually***, when debugging code. Biological Literacy ------------------- Biology from the molecular to ecosystemic levels is intertwined with our lives. Evaluating reports on problems of this magnitude requires critical thinking. ### Wait... what's Critical Thinking? Ideally, when parsing new information, think like this: - Is the information consistent with info from other sources? - How reliable is the information? - Is the author credible? - Where was the information published? - Was the information obtained through proper scientific procedures? - Were experimental results interpreted correctly? - Are there other possible explanations for the results? ### Science as a Social Activity Science is not fixed. It changes. At any given time, scientists are drawing conclusions from the data they have at that time.\ As we ask different questions or use improved data or technology, the data they have access to ***changes***, therefore their conclusions changes. ### Limitations of Science - Controls are typically not 100% possible, especially when an experiment is being conducted in nature. - There are limitations to the type of questions that can be answered by scientific inquiry, because they require hypotheses to be testable and falsifiable. - Science is ***devoid*** of moral content: There's no "right" or "wrong". - There are many questions that lie outside the realm of science -- for example, supernatural phenomena nor religion can be proven or disproven via scientific examination. Review Activity -- Scientific Method Exercise --------------------------------------------- Review the following to make sure the following hypotheses are testable and falsifiable. - ***Increasing numbers of deformities such as extra limbs that have ben noted in many frog populations in North America are caused by infections by trematodes (parasitic flatworms).*** - ***Testable and falsifiable.*** It can be proven and disproven, and it can be tested by setting aside a control group not infected by the trematodes. - ***People with strong religious beliefs live more meaningful lives***. - ***Non-testable and non-falsifiable.*** Several vectors of which you'd have to take a person at their word for the data you receive, and *people lie.* A lot. - ***People are more likely to survive cancer if they have a positive attitude.*** - ***Non-testable and non-falsifiable.*** What do we *define* as a positive attitude? Furthermore, is it repeatable or ethical to run these tests on dying cancer patients? - ***Humans and chimpanzees diverged from a common ancestor that lived 5-7 million years ago.*** - ***Non-testable and non-falsifiable.*** We cannot get any concrete data on our ancestors of 5-7 million years ago that would suggest this. Although this line of thinking is in line with the Theory of Evolution, it cannot be tested. - ***Corn seedlings grow more quickly when people talk to them.*** - As dumb as it sounds, ***testable and falsifiable.*** You can test this theory by isolating two groups of corn seedlings and checking whether the ones you talked to or didn't talk to grew higher. - ***If you live a good life, you will be rewarded with an eternity in Heaven***. - As much as I'd like to oppose, ***non-testable and non-falsifiable,*** for obvious reasons. Chapters 2 and 3 -- The Chemical Basis of Life ============================================== Overview -------- ### The Chemistry of Life In ***The Chemistry of Life***, we'll go over the elements required by living things. Life requires about 25 elements. Atoms (you already know this from Chem 11) are formed from protons, neutrons, and electrons. Elements bond to form molecules. ### The Water Molecule In ***The Water Molecule***, we'll go over Hydrogen Bonding, acids, bases, and buffers. We'll go directly into why water, specifically, is the basis of life, based on its chemical composition. ### Carbon and the Molecular Diversity of Life In ***Carbon and the Molecular Diversity of Life***, we'll be going over why Carbon is the key element in life on earth, macromolecules, carbohydrates, lipids, proteins, and nucleic acids. The Chemistry of Life --------------------- ### Biological Function at the Chemical Level All the properties of organisms depend on how atoms are arranged in molecules, and how said molecules are arranged in cells. There are, however, emergent properties of life composed of millions and millions of atoms that cannot be grasped simply by looking at the field of chemistry. There's a strong relationship between structure and function at all levels of life. What a chemical structure ***looks like*** typically reveals ***what it does***. For example, the specific arrangement of atoms in a molecule of chlorophyll allows it to absorb light. ### The Essential Elements of Life Organisms are composed of matter, and matter is anything that takes up space and has mass. Chemical elements are substances that only contain one type of atom. Throw away that *Fullmetal Alchemist* list of trace elements in the body -- it's completely wrong. There are 25 of the 92 natural occurring elements that are essential to life. Trace elements are required by an organism in minute quantities. #### Atoms You already know this: Protons, neutrons, and electrons. Protons are positively charged, neutrons aren't charged at all, and electrons are negatively charged. Each element is defined concerning the distribution of subatomic particles. Let's take for example, Carbon: ![A blue square with black text and a black letter Description automatically generated](media/image2.png) Carbon's atomic number is placed in the top left corner of its block -- The atomic number is the number of protons in its nucleus, and an atomic number is unique to any single element. An atom's **atomic number** is the number of protons and neutrons in the atom. It's noted in the top right corner in the example. ##### Isotopes Isotopes are elements that have the same atomic number but differ in numbers of neutrons. Carbon-12 is the stock-standard carbon and the most abundant variation of carbon, but Carbon-13 and Carbon-14 have 7 and 8 neutrons respectively. Carbon-14 is ***radioactive***. Radioactive isotopes decay spontaneously and give off particles and energy in order to become stable. (The time this takes is typically known as a Half-Life, signified by a lambda) They're dangerous to life because they can cause DNA mutations, but they can also be useful in biological research and medicine as tracers. Living cells cannot distinguish radioactive isotopes from nonradioactive atoms of the same elements. ##### Electrons Electrons typically dictate how an atom behaves when it encounters other atoms. Electrons in an atom occur at certain energy levels known as electron shells. The farther an electron is from a nucleus, the more energy it has (Of course, because of repulsive forces between Protons and Electrons, these Electrons stay close solely because their basically irrelevant mass is drawn in by the comparatively overwhelming mass of the protons and neutrons generating microgravity). ##### Valence Electrons Valence electrons... you already know this, are in the outermost shell of an atom. The chemical behaviour of an atom is determined by the fullness of the ***valence shell*** of an atom. A full valence shell (e.g., Noble Gases) means that an atom is chemically *inert.* ##### The Octet Rule In the formation of molecules from atoms, most atoms attempt to achieve a configuration of 8 valence electrons around each atom. ### Compounds Compounds are substances containing 2 or more different elements in a fixed ratio. They have characteristics different from those of its elements. Most compounds in living organisms contain at least 4 elements, and a different arrangement of atoms determines the unique properties of each compound. ### Chemical Bonds Four types of chemical bonds: - Covalent: Literally what it sounds like (co-valence) when atoms share electrons within their valence shells. All non-ionic bonds are covalent in nature. - Polar Covalent Bonds: Covalent bonds where shared electrons are pulled closer to the more electronegative atom - Non-Polar Covalent Bonds: Covalent bonds where electrons are shared equally between atoms (H~2~, O~2~, CH~4~) - Ionic bonds: When atoms hand over their electrons to another atom and become ions. There are anions ( atoms with more electrons than they usually have -- negatively charged) and cations (atoms with less electrons than they usually have -- positively charged). Ionic bonds form between Group 1/2 metals and nonmetals from Group 16/17. - Hydrogen Bonds: We'll get to this later in *Water as a Polar Molecule.* - Van der Waals interactions: Not important to BIOL 1111. The Water Molecule ------------------ Water is the primary biological medium on earth. All living beings require water more than any other substance. Most cells are surrounded by water, and cells themselves are 70-95% water. The abundance of water on earth makes it habitable to living beings. Water is made up of two kinds of atoms with differing electronegativity. Oxygen attracts elements more strongly than Hydrogen. ### Water as a Polar Molecule H~2~O, even though it is neutral overall, has a slightly negative pole and two slightly positive poles, making it a polar molecule. Water's polarity leads to Hydrogen Bonding and other unusual properties. A diagram of a molecule Description automatically generated #### Hydrogen Bonds On Water, the charged region on each molecule attracts oppositely charged regions on neighboring H~2~O molecules, forming weak bonds called Hydrogen bonds. ### Emergent Properties of Water ***SFAT*** There are four emergent properties of water that contribute to Earth's ability to support life, and they're all related to the hydrogen bonds that form between water molecules. - Cohesive Behavior: Hydrogen bonds hold water molecules together, allowing water to be much more cohesive than other substances. - Take, for example, a tree. It has no veins or organs forcing water up from the roots to the top of the tree, where cells might need it most. Because Water is cohesive, when it evaporates, it takes other molecules with it due to its bonding, allowing it to transport itself upwards in a chain. - Temperature moderation: Water has the ability to moderate temperatures, keeping them within limits that permit life. It absorbs heat from warmer air and releases stored heat to cooler air. - When water is heated, the energy first disrupts Hydrogen bonds and makes molecules move faster, and heat is absorbed to do so. Conversely, when water is cooled, more hydrogen bonds form, and heat is released. - Negative Thermal Expansion: Water expands upon freezing. Ice floats. Weird, isn't it? If ice sank, all bodies of water would eventually freeze solid, and life on earth would be impossible. The reason why it floats is because the hydrogen bonds in ice are more ordered than in liquid water. (This shouldn't be anything new. We see it in snowflakes, micropatterns in ice, and so on, and so forth, also energy levels dictate the orderliness of atoms within a substance). - Solvent Versatility: Water is known as the ***universal solvent***, due to its size and polarity allowing it to dissolve many substances. Anything polar will dissolve in water. We call these substances *hydrophilic*, and their opposites, *hydrophobic.* ### Acids and Bases Life's chemistry is sensitive to acidic and basic conditions. In aqueous solutions, water molecules will break into OH^-^ and H^+^ ions. In order for things to function properly within an organism, these ions must be balanced properly. In water, due to the ratio of Hydrogen to Oxygen, the balance of these ions are equal. ### The pH Scale Used to describe the acidity of a solution. Ranges from 0 (most acidic) to 14 (most basic). Biological fluids typically range from 6 to 8. Our ranges as biological organisms must stay very close to 7 or else we'll straight up wither away. ### Buffers Buffers are substances that make sure we stay close to this range. They minimize changes in concentrations of H^+^ or OH^-^ in a solution. ### Chemical Reactions and Matter Chemical reactions break up bonds and remake them. Diatomic molecules like H~2~ and O~2~ will break up their existing bonds to form H~2~O. Carbon and the Molecular Diversity of Life ------------------------------------------ ### Cell Molecules Life's diversity results from a variety of molecules, derived from a small number of basic structural patterns. Almost all molecules created by cells are composed of carbon atoms bonded to one another and to atoms of other elements (especially Hydrogen, Oxygen, and Nitrogen). Carbon is very good at forming large and diverse molecules. Cell-synthesized compounds containing carbon are known as ***organic molecules***. Proteins, DNA, Carbohydrates, and others are all composed of carbon compounds. ### The Carbon Skeleton Molecular diversity arises from variation in the carbon skeleton. Basically, there are a lot of complex chemical structures that use Carbon as a backbone, like Ethane, Butane, Propane, and Methylpropane. ### Hydrocarbons Hydrocarbons are organic molecules consisting of only Carbon and Hydrogen. Many organic molecules like fats have hydrocarbon components. Hydrocarbons undergo reactions that release lots of energy. You're familiar with this as ***combustion*,** in, for example, your car or a simple fuel engine in which hydrocarbon bonds are broken in order to release energy. Hydrocarbons are very hydrophobic, because they form nonpolar covalent bonds. ### Functional Groups Distinctive properties of organic molecules depend on the carbon skeleton and the molecular components attached to it. Organic molecules *might* have one or more functional groups attached to them. ![A diagram of a group of molecules Description automatically generated with medium confidence](media/image4.png) All functional groups are *polar*, making them hydrophilic and soluble in water. #### Aldehyde Aldehyde is a ***terminal carbon*** (A carbon at the end of a carbon chain, on say, a Hydrocarbon) double-bonded to Oxygen and single-bonded to Hydrogen. #### Carbonyl Carbonyl is a non-terminal carbon double-bonded to Oxygen. #### Carboxyl Carboxyl is a terminal carbon double-bonded to Oxygen and single bonded to Hydroxide. #### Phosphate PO~4~. Bonded to the end of an organic molecule. #### Hydroxyl Hydroxide bonded to the end of a carbon chain. \*come back to this for Sulfhydryl and Amino later ### Carbon Structures A diagram of a chemical structure Description automatically generated Prepare to see a lot of this. Every vertex (corner) on one of these is a Carbon. That means, the double-bonded Oxygen on the end of Testosterone is a Carbonyl. The lines on the inside are ***double bonds***. Macromolecules -------------- ### Large Biomolecules Cells make many large biomolecules from a small set of smaller molecules. Macromolecules are large molecules composed of thousands of covalently connected atoms. There are ***four*** classes of macromolecules: - Polysaccharides (known as carbohydrates) - Lipids - Proteins - Nucleic Acids ### Monomers and Polymers Cells make large molecules by joining smaller organic molecules into chains known as ***polymers***. A ***polymer*** is a large molecule consisting of many identical or similar molecular units strung together. A ***monomer*** has units that serve as building blocks of polymers. There are ***trillions*** of different polymers made up of 40-50 monomers. The infinite amount of proteins are made up of 20 amino acids, and DNA is made up of only 4 nucleotides in a sequence N nucleotides long. So, the possible DNA combinations are 4^N^. ### How To Build Your Own Polymers Cells link monomers together to form polymers via dehydration synthesis. Monomers have Hydrogen and Hydroxide on either end of them. To join two monomers into a polymer, the Hydrogen and Hydroxide are combined in order to form water, leaving the monomers joined into a longer polymer. ![A diagram of a reaction Description automatically generated](media/image6.png) The reverse is used to break down polymers into monomers -- the ingredients for water that they *lost* are added back to them, thus, water breaks down polymers. ### Carbohydrates Carbohydrates include sugars and their polymers. The simplest carbohydrates are called monosaccharides, or, single sugars. Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks. ### Monosaccharides Monosaccharides are the simplest carbohydrates. They form always in the configuration of C~N~H~2N~O~N~. Glucose (C~6~H~12~O~6~) is the most common monosaccharide. Monosaccharides are the main fuel molecules for cells to do work. Their bonds are good at storing energy. Our cells absorb glucose and use it to make ATP, which is energy for the cell. ### Disaccharides Cells link sugars into disaccharides. For example, sucrose is a disaccharide composed of glucose and fructose. A diagram of a chemical reaction Description automatically generated ### Polysaccharides Polysaccharides are polymers of hundreds or thousands of monosaccharides linked via dehydration reactions. #### Starch Starch is a *storage* polysaccharide for plants. It consists of glucose monomers that are mostly unbranched, and helps plants store energy in a solid form. #### Glycogen Glycogen is like starch, but for animals. Glycogen helps store glucose in liver and muscle cells. It's identical to starch, but more compact and branched. #### Cellulose Cellulose is a structural polysaccharide in plants, and the main component of cell walls. It's also made of glucose but linked differently than starch and glycogen. It's the most abundant organic material in the world. Cellulose forms linear chains Hydrogen bonded to each other to form fibers. Only certain micro-organisms and some fungi can *hydrolyze* (verb: break down by chemical reaction with water) cellulose. #### Lipids Lipids are composed of carbon and hydrogen atoms linked via nonpolar bonds. The unifying feature of lipids is that they are *hydrophobic*. They exist in fats, phospholipids, and steroids. Lipids are the one class of macromolecules that aren't composed of linked monomers. ##### Fats Triacylglycerol. ![A black lines with numbers Description automatically generated with medium confidence](media/image8.png) Same rule as the hexagons -- each vertex is a Carbon. Fats are used in the body for LTES -- Long Term Energy Storage. They're 2x better than starch, or *glycogens*, at this. ##### Fatty Acids Fatty acids vary in length (the number of Carbons) and in the number and location of double bonds. Saturated fatty acids have the maximum number of Hydrogen atoms possible and no double bonds, hence, the name, *saturated*. Unsaturated fatty acids have one or more double bonds. They're liquid at room temperature and are mainly derived from plants. They can be *cis or trans*. The plant-basing should be a hint as to why they're more recommended in your diet over saturated fatty acids. Unsaturated fatty acids tend not to accumulate in your blood vessels, so unlike saturated fatty acids (and trans fats), they're recommended in your diet. #### Phospholipids Phospholipids have a phosphate group that replaces one fatty acid. Phospholipids are *amphipathic (*adjective: having both hydrophilic and hydrophobic regions). These form bilayers, the bases of cellular membranes. #### Steroids Steroids are lipids with carbon skeletons bent to form 4 fused rings. All steroids are made from cholesterol as a starting molecule. Examples of steroids are vitamins, bile acids, and hormones. ### Proteins Proteins are the doers in cellular biology. They're essential to the structure and activities of life. There are seven classes of proteins: - Structural (silk, hair, tendons) - Contractile (Actin, Myosin) - Storage (ovalbumin) - Defensive (antibodies) - Transport (hemoglobin) - Signaling proteins (hormones) - Enzymes For the sake of BIOL 1111, all enzymes are composed of proteins. #### Enzymes Enzymes are proteins that serve as chemical catalysts. For example, the *sucrase* enzyme breaks down sucrose substrate into glucose and fructose. Asking that to be done on its own, it would take 10,000 years. With sucrase, it takes 10 minutes. #### Proteins as Linked Amino Acids The monomers of proteins are amino acids. There are 20 different amino acids, all with the same general structure, but different "R" groups. Different proteins vary in length and in the sequence of amino acids. Said sequence and shape determines protein function. #### Protein Form and Function Protein shape is largely determined by its amino acid sequence. In addition to this, the sequence of amino acids, physical, and chemical conditions can affect its structure. Altering the pH, salt concentration, temperature, or other factors can cause a protein to unravel. This phenomenon, where a protein loses its native structure, is called ***denaturation***. Denatured proteins are biologically inactive, but if you put them in a state where they are no longer bombarded by the wrong conditions, they'll ***renature,*** folding themselves back into the right shape and form. ### Nucleic Acids Nucleic acids are macromolecules that encode information required to build proteins. The sequence of nucleotides determines the sequence of amino acids along a polypeptide chain. There are two types of nucleic acids: DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) Nucleic acid polymers are called ***nucleotides***. #### Nucleotides Nucleotides all have the same general structure: ![A diagram of a molecule Description automatically generated](media/image10.png) ***SFAT: PAY ATTENTION TO A FEW THINGS:*** Nucleotides contain a Phosphate Group. Many BIOL 1111 students confuse it with a glucose because of the ring structure, but this isn't the case. DNA is composed of 4 different types of nucleotides: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). #### DNA DNA is formed of two strands that come together to form a double helix. The two strands are held together by hydrogen bonds according to two rules: - Adenine will pair with Thymine and ***nothing else***. - Cytosine will pair with Guanine and ***nothing else.*** ***SFAT***: You should be able to fill in the blanks in a DNA sequence given one side of a double helix. This brings us to the end of *The Chemical Basis of Life* as a unit. You should come back later today to review these notes and make sure they're well-understood. Then, replicate as many of them on either Sticky Notes or paper to test your own understanding. Are we good to go? Good. Chapter 4 -- A Tour of the Cell =============================== Overview -------- In *A Tour of the Cell,* we'll be investigating the cell as the *fundamental unit of life*. All organisms are made of cells, and the cell is the simplest collection of matter, classified as *living.* For one to understand how organisms work, they must understand how cells work. Cells were first observed by Robert Hooke in 1663, while looking through a low-quality microscope at cork. He found structures that he coined cells, due to their blocky, jail-cellblock like structures. Form and Function ----------------- The smallest cells are mycoplasma, of domain Bacteria. They are 0.1-1 micrometer in diameter. The largest cells are bird eggs, and the longest cells are muscle or nerve cells. The takeaway here is that cells' form and function are related, like with proteins and other macromolecules. Units of Length by Biologists ----------------------------- When discussing cells, typically, most of them that we'll be discussing are within the micrometric range. From Single Cells to People ![A close-up of a cell Description automatically generated](media/image12.png) ---------------------------------------------------------------------------------------------------------- We all began as one single fertilized cell, called a *zygote*. Very rapidly, this cell divides, and divides, and divides, and divides.... Until it forms a foetus, which eventually, forms a human being. So, wait -- why are cells so small, anyway? ------------------------------------------- Natural laws limit the size of cells. At minimum, cells need to be large enough to house the parts it needs to fulfill the *Seven Characteristics*. The largest a cell can be is limited by the amount of surface it needs to obtain nutrients from the environment and dispose of waste. Think of the *Tsiolkovsky Rocket Equation* -- larger spacecraft need more fuel to propel themselves to escape velocity. So, cells often descend to the optimum size for their function to be optimized by their form. A diagram of a large cube Description automatically generated A small cell has a greater ratio of surface area to volume than a large cell of the same shape. Characteristics of Every Cell ----------------------------- So, every cell has: - A plasma membrane. It's their barrier between the internal environment and the external environment. It controls what can and can't permeate in and out of the cell. - Chromosomes. They're strands of DNA that carry its genes. - Ribosomes. They make proteins according to genetic instructions. - Cytoplasm. The interior mushy bits of the cell. In eukaryotic cells, cytoplasm is the space between the nucleus and the plasma membrane. The Two Types of Cells ---------------------- ### Prokaryotic Cells Prokaryotic cells are small, and simple. They don't have nuclei or membrane-bound organelles. They're typically 1/10^th^ the size of a eukaryotic cell and have much less DNA. Prokaryotes are enclosed by a plasma membrane and are encased in a rigid cell wall, unlike our cells. (Note that this cell wall differs from the cell wall found in plant cells. More on that, later.) Inside prokaryotes, the DNA is contained in a nucleoid region, exclusive to Archaea and Bacteria. It's in direct contact with the cell cytoplasm. On the exterior surface of the cell, there are processes called pili (tiny little hairs that allow them to attach to surfaces) and flagella (tiny little rotor-like hairs that allow them to swim around in an environment). ### Eukaryotic Cells Eukaryotic cells are larger and more complex. They have nuclei, cytoskeletons, and membrane-bound organelles that have distinct functionality. They have more DNA (larger genomes), and are found in animals, fungi, and protists. Eukaryotes are highly compartmentalized -- they are more efficient, able to process opposing chemical reactions at a higher rate, keep cooperating enzymes close together, and have higher local concentrations of molecules. Animal vs. Plant Cells ---------------------- Animals and plants have more of the same organelles, but have a few differences: Animal cells have: - Lysosomes - Centrioles - Flagella Plant Cells have: - Chloroplasts -- the structures responsible for photosynthesis. - A rigid cell wall (not like the one found in Prokaryotes). - A central vacuole -- water storage for the plant cell. More on this later. Eukaryotic Cell Structures -------------------------- We're done with bacteria -- for now. Now, we discuss structures of the Eukaryotic cell. ### Plasma Membrane Plasma membranes are flexible, sturdy barriers that surround the cytoplasm of a cell. They're ***phospholipid bilayers*** (noun: a thin polar membrane made of two layers of lipid molecules) with embedded proteins. ### The Nucleus The nucleus is the largest organelle at typically \~5 nanometers. It is the cell's genetic control center. The nucleus is separated from the cytoplasm by the ***nuclear envelope***. Nuclear pores on the nucleus regulate entry and exit of material. The ***nucleolus***, deep inside the nucleus, is the region inside the nucleus that produces ribosomal RNA. In the nucleus, DNA and proteins form genetic material called ***chromatin***. Here's how this is done: DNA is wrapped around a protein called ***histones***, making ***chromatin fibers***, which are looped and arranged into chromosomes. This process happens during cell division. Typically, the DNA isn't discretely visible within a normal cell, but is visible after chromosomization. Think of zipping up a setup.exe and sending it to a friend, so they can unzip it for their PC to execute the instructions inside. ### Ribosomes Ribosomes make proteins using data from mRNA and raw materials in the form of Amino acids. The Central Dogma of Biology ---------------------------- ***SFAT***: This is very important. The Central Dogma of Biology describes how information flows within a cell. Most of your DNA encodes for "how to make X or Y protein". In order to start making this, your DNA needs to transcribe parts of itself into Messenger RNA inside your nucleus. Once this is done, it exits a nuclear pore and is read by a ribosome, which combines amino acids into the protein the mRNA codes for. Think of the DNA like source code, the RNA like a middle representation created by a compiler preprocessor, and the protein like the machine code executable created from the representation by the compiler. ***This is the cutoff for Midterm 1. Now would be a good time to start reviewing everything from* Introduction to Biology *all the way to* The Central Dogma of Biology.** -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The Endomembrane System and its Organelles ------------------------------------------ The Endomembrane System is a collection of ***membranous*** (adj. concerning the membrane of the cell) organelles. These organelles manufacture, distribute, and break down cell products. The Endomembrane System includes: - Nuclei - The Endoplasmic Reticulum - The Golgi Complex - Lysosomes - Vacuoles - The Plasma Membrane Keep in mind from [the Central Dogma](#the-central-dogma-of-biology) that the Nuclei is not only the DNA holder, but the site of mRNA production. ### Endoplasmic Reticulum The endoplasmic reticulum is a membrane that is continuous along the nuclear envelope. It's a network of membrane clearly visible next to the nucleus. Its interior space is distinct from the cytoplasm. There are two types of ER, distinguished by the presence or absence of ribosomes: ***rough*** and ***smooth*** endoplasmic reticulum. #### Rough Endoplasmic Reticulum Ribosomes on the surface of Rough Endoplasmic Reticulum produce proteins destined to be on the cell's outside or the cell's surface. The protein created by the ribosome on the RER's surface enters inside the rough endoplasmic reticulum, where it has glycoprotein added to it. Once it's modified like this, it's going to leave the RER within a ***vesicle*** popped off the RER. Think of this like a shipping container. #### Smooth Endoplasmic Reticulum Smooth endoplasmic reticula synthesize lipids and membranes. They also store calcium. ### Golgi Apparatus The Golgi apparatus (or Golgi complex, or Golgi body, or just Golgi) consists of stacks of membranous sacs. They receive and modify products from the Endoplasmic Reticulum, and then send said products on to other organelles or to the cell membrane. Proteins that pass through the Golgi apparatus have one of three destinations: - Lysosome - Embedding in the plasma membrane - Excretion outside of the cell ### Lysosomes Lysosomes are sacs of digestive enzymes budded off the golgi apparatus. They fuse with food vacuoles created by ***phagocytosis*** (noun: process by which certain living cells called phagocytes ingest or engulf other cells or particles) or ***autophagy*** (noun: A process by which a cell breaks down and destroys old, damaged, or abnormal proteins and other substances in its cytoplasm). They hydrolyze proteins, fats, polysaccharides and nucleic acids. Lysosomes also help retire old organelles, such as mitochondria, by attaching to and ***recycling*** them into base materials so they can be remade by the cell. ### Vacuoles Vacuoles (***not*** vesicles) are the cell's storage chest. Like a plant cell's central vacuole that stores water, general vacuoles store material for the cell to use. ### Mitochondria ~~The powerhouse of the cell~~. They convert Oxygen and Glucose into Water and Adenosine Triphosphate (ATP). C~6~H~12~O~6~ + 6 O~2~ =\> 6 CO~2~ + 6 H~2~O + ATP ### Chloroplasts Depicted as green in most diagrams because of their abundance of chlorophyll. Here's the chemical formula for photosynthesis: 6 CO~2~ + 6 H~2~O =\> C~6~H~12~O~6~ + 6 O~2~ ### Peroxisomes Peroxisomes are specialized metabolic compartments. Basically, they convert substances called ***reactive oxygen species*** (crazy substances that can corrode DNA, accidentally created by your cells by metabolism) into water. ***Important SFAT Header: Try to be able to name all these organelles and their functions in one or two words.*** Structures Responsible for Cell Support, Movement, and Communication -------------------------------------------------------------------- ### The Cytoskeleton The cytoskeleton is a cell skeleton, or a network of fibres, that run throughout the cell. Its function is to: - Establish and maintain cell shape - Provide mechanical strength to the cell - Enable cell locomotion - Separate chromosomes during cell division - Transport organelles between cells Cytoskeletons are made of: - Microfilaments (also known as Actin) that allow cells to change shape and move. - Intermediate filaments that reinforce cells and anchor certain organelles - Microtubules that give the cell rigidity, provide anchors for organelles, and act as tracks for organelle movement Cells move via microfilaments by ***polymerizing*** and ***depolymerizing*** actin, stretching it out and moving it back in. #### Cilia and Flagella A cilia or flagellum is composed of several microtubule filaments in a particular pattern. When microtubules bend, the cilia and flagella move. #### Microfilaments Microfilaments that function in ***cellular motility*** (m. noun: the spontaneous movement of a cell from one location to another by consumption of energy) contain ***myosin*** in addition to actin. #### The Extracellular Matrix The extracellular matrix is the environment in which cells live within a body. It's a sticky layer of glycoprotein that binds cells into tissues. It also has protective and supportive functions. ### Cell-To-Cell Junctions Cells, as you know, are typically capable of living on their own, but a lot of them in animals like us, interact with others through *cell-to-cell junctions*. #### Tight Cell Junctions Tight junctions bind cells into leakproof sheets. Meaning, nothing can get through that junction -- not water, material, etc. #### Anchoring Cell Junctions Anchoring cell junctions link animal cells to one another. #### Gap Junctions Gap junctions allow substances to flow from cell-to-cell. #### Plant Cell Walls and Junctions Plant cell walls are largely made of cellulose. They are connected via ***plasmodesmata*** (roots: *plasmo-*, for formation -- *desma-*, for bond, therefore *plasmodesma*, plural *plasmodesmata,* for *a formed bond*.) This brings us to the end of ***A Tour of the Cell***. Are we good to go? Good. Chapter 5 -- Cell Function ========================== Membrane Structure ------------------ ### The Cell Membrane The cell membrane is a selectively permeable, amphipathic structure. The lipid bilayer is overwhelmingly hydrophobic. The Cell membrane is a fluid mosaic of lipids and proteins. Lipid molecules form a flexible bilayer, and protein molecules are embedded in the plasma membrane. Carbohydrates act as cell identification tags on the surface of the bilayer. ### Membrane Fluidity Cell membranes have the consistency of salad oil at room temperature. Lipids have rapid lateral movement and flip-flop rarely. Flip-flopping is rare because it asks the polar head of a lipid to pass through a hydrophobic region and come out the other side. Very rare. Membranes ***need*** sufficient fluidity to function. ### Fluidity and Lipid Composition Saturated fatty acids have single-bonded carbons. This straight chain allows maximum interaction. They're solid at room temperature, and their lipid hydrocarbon tails are mostly straight. Unsaturated fatty acids have double-bonded carbons. They're liquid at room temperature. Their bent chains space lipid tails apart. A mix of both saturated and unsaturated fatty acids maintains the cell membrane's semi fluidity. ### Cholesterol Cholesterol is embedded in cell plasma membranes, as a ***fluidity buffer***. It makes sure that the cell membrane stays at the sweet spot of fluidity. At warm temperatures like 37C, cholesterol restrains lateral movement of phospholipids. At cool temperatures, cholesterol makes sure that phospholipids don't pack too tightly together. ### Membrane Proteins A membrane is a mosaic of different proteins embedded in in the lipid bilayer. Peripheral proteins live entirely on the membrane surface and have ionic and hydrogen bond interactions with hydrophilic lipid and protein groups. Integral proteins possess hydrophobic domains that are anchored to hydrophobic lipids. Transmembrane proteins span the membrane and contain both hydrophobic and hydrophilic regions. #### Membrane Protein Functions Membrane proteins do a few things: - Transport: They can transport in and out ATP, - Enzymatic activity: - Signal transduction: They can take in signalling molecules into the cell so that it knows where it is within the environment. - Cell-to-cell recognition: Helps other cells know what this cell is. #### Membrane Carbohydrates Carbohydrates are found on the exterior surface of a cell membrane. They provide *specificity* for cell to cell or cell to protein interactions. Membrane Transport ------------------ The cell membrane controls intracellular traffic by being selectively permeable. It allows some substances to cross, but not others. The cell membrane is largely hydrophobic, so hydrophobic molecules dissolve in the lipid bilayer and pass through the membrane rapidly. Polar molecules and ions do not pass so easily. ### So, what makes the membrane selectively permeable? Transport proteins. They span the membrane, and each transport protein is specific to one solute. Some are ***channels***, others, ***transporters***. Polar molecules and ions typically pass through these, since they can't pass through the hydrophobic cell membrane naturally. ### Passive Transport ***SFAT*** ***STATEMENT I: Diffusion*** is the tendency for solutes of any kind to spread out spontaneously from any area of high concentration to an area of low concentration. In ***simple diffusion***, the substance has to be hydrophobic and requires no energy to spread itself out. These particles do not care about the general "fullness" of an area. They will move from one area of high concentration ***of their own kind*** to an area of low concentration. In other words, no solute will ***ever*** care about what another solute is doing. This statement is more Physics than Biology, so just take it at face value for now. ### Osmosis ***STATEMENT II:*** Water will always move from an area of low solute concentration to an area of high solute concentration. Osmosis is the diffusion of water across a selectively permeable membrane. Effectively, what Statement II is describing is a ***solvent***'s tendency to move towards where the most ***solute*** is. ***SFAT:*** You need to be able to repeat both Statements I and II off the dome. Got it? ### Cell Behaviour in Different Environments There are three behaviours in this topic: [***hypertonic, hypotonic, and isotonic***. ] Hypertonic solutions refer to an abundance of saltiness in a solution. Hypotonic solutions refer to a deficiency of saltiness in a solution. Isotonic solutions refer to an equality between saltiness and solvent in a solution. Many marine animals are [isotonic] to sea water. If our cells were in those environments, eventually they would dehydrate due to Statement II, shrink, and die. Marine animal cells, however, are *isotonic* to the environments that they live in. This is why certain animals die if you put them in salt water and others die if put in fresh water. #### Osmoregulation Osmoregulation is the control of water/salinity balance. Osmosis causes cells to ***shrink*** in a hypertonic solution because the water will move out of the cell to a high solute concentration. In a hypotonic solution, the water will move from the environment into your cells, causing them to ***swell and burst.*** Both are due to *Statement I/II.* #### Plant Cells and What Makes Them Happy Plant cells are different from other cells in a few regards. Plant cells are happiest in ***hypotonic*** (not-so-salty) environments where they take on a lot of water because their cell wall prevents them from rupturing. This makes them become ***turgid***. ### Facilitated Diffusion Recall what we were saying about the lipid bilayer. Hydrophobic (nonpolar) substances can move in and out of it easily because the bilayer is also largely hydrophobic. ***Facilitated Diffusion*** is when substances that *are* polar move through the bilayer through embedded ***transport proteins***. It's a passive transport system, meaning that it's moving from a place of high concentration to low concentration (diffusion), therefore, it requires no energy. In MMC terms, think of a kitchen sink outputting 2400 mB/s without a pump. #### Active Transport Transport proteins are capable of moving solutes across a membrane *against Statement I*, meaning that they'll move to an area of higher concentration. Of course, since it's against diffusive laws, it requires ATP to do so. This is what is known as ***Active Transport***. In MMC terms, think of a BuildCraft Oil pump or Quarry transporting material if it's powered. #### Bulk Transport ***Exocytosis*** (m. noun: The movement of large molecules or particles to the outside of the cell) happens when a vesicle fuses with the membrane and expels its contents. ***Endocytosis*** is the opposite, when a vesicle pops off of the membrane after sucking in a bunch of particles. Energy and the Cell ------------------- Chemical reactions take place in cells as well as their membranes. Living cells transform energy by means of enzyme-controlled chemical reactions. For the sake of BIOL 1111, Energy is the ***ability to perform Work.*** ### The Forms of Energy Recall from Physics 11: There are two forms of energy, ***Kinetic*** (the energy that is doing work, the energy that an object possesses because it is actually doing something like movement) and ***Potential*** (the energy that is stored in a system due to its position, like the stored energy in a battery, a series of hydrocarbons, etc.). We term potential energy in BIOL 1111 as ***Chemical Energy***, the potential energy of molecules. The actual energy portion is stored in a molecule's ***chemical bonds***. ### Organisms' Energy Transformations Chemical energy is used when a reaction releases the potential energy in a molecule's bonds, and it's transformed into kinetic energy. For example, burning gas releases energy from the gasoline to drive the engine. ### Systems and Thermodynamics ***Thermodynamics*** is the study of energy transformations. A ***System*** is the collection of matter under study. A system can be open or closed, with a closed system being isolated from its surroundings, and an open system exchanging both matter and energy between its surroundings. We, human beings, are **open** systems. ### Laws of Thermodynamics ***The First Law of Thermodynamics*** is the Law of Equivalent Exchange: ***Energy can be changed from one form to another, but never created or destroyed.*** Ergo, energy cannot ever magically appear or disappear. If you seem to be losing or gaining energy in any sort of transfer or reaction, then it's going to or coming from somewhere. The energy of the universe stays constant. There's no more than from when it started. Speaking of losing or gaining energy, the ***Second Law of Thermodynamics:*** ***Energy changes are never 100% efficient. Conversions increase disorder, or entropy.*** Ergo, ***the randomness of the universe will always increase.*** Although the net energy of the universe does not change, not all of it is available to do work. Entropy is defined as the ***energy of randomness***. Think of how your bedroom will eventually fall into disorder if it's not consistently cleaned using Energy to do Work, but, of course, entropy comes all the same. ### Cellular Metabolism There are two general types of reactions in Cellular Metabolism: ***Catabolic Pathways*** release energy by breaking down complex molecules into simple compounds. They are ***exergonic***, meaning that they release energy. ***Anabolic Pathways*** consume energy to build complex molecules from simpler ones. They are ***endergonic***, requiring energy to do work. Take, for example: The above digestion of dietary proteins is catabolic, releasing energy. The above creation of body proteins is anabolic, requiring energy. ### Adenosine Triphosphate Energy coupling in cells is mostly mediated by ATP, Adenosine Triphosphate. Like polymers, ATP is activated to make energy through hydrolyzation reactions. When ATP is hydrolyzed, it's split into Adenosine Diphosphate and a lone phosphate, releasing energy. ATP is renewable. When exergonic reactions release energy, that energy is stored in ATP molecules, then expended, transforming into ADP + P. When you eat, the ADP +P becomes ATP, which stores the energy, and so on. ![A diagram of a cycle Description automatically generated](media/image16.png) ### Enzymes Enzymes help speed up the chemical reactions required for life. Without them, these reactions would take millions upon millions of years, too slow for our biological clocks to run in lockstep with. Enzymes are selective, meaning that they only bind to certain substrates. Their specificity is due to their shape. The ***active site*** is the place on an enzyme where a substrate binds. Each cell has thousands of different enzymes, each performing a specific chemical reaction. They function optimally at a specific temperature, pH, and salt concentration. This brings us to the end of ***Cell Function***. Are we good to go? Good. Be sure to come back and go over these notes, filling in anything you missed from the slides. ***This is the cutoff for Quiz 2 -- Get going!*** ------------------------------------------------- Chapter 16 -- Nutrition ======================= Overview -------- *Nutrition* will be covered in two parts. In Part 1 of the same name (which we'll be calling *Intro to Nutrition* to avoid confusion), we'll be talking about dieting, obesity, healthy lifestyles, and essential nutrients. In Part 2, *The Human Digestive System*, we'll be talking about how we obtain and process foods, and the human digestive system in larger detail. Intro to Nutrition ------------------ ### The Needs for a Healthy Diet Animal diets must contain: - Fuel for its activities - Raw materials for making the body's molecules - Essential nutrients that the body cannot fabricate itself. ### How do we use our nutritional energy? Animals require energy for their cells to do work. ***75%*** of this energy is for maintenance and is what a resting animal needs to survive, used for heating, cooling, and digestion. ***25%*** of this energy is used for extra activity: standing, thinking, sleeping, and sports. (keep in mind, 1 Calorie (with a big C) is 1000 kcal.) ### More on Calories The Calorie is a unit that describes the potential energy content of food. It tells us how much cell work can be powered by the energy released by breaking down that food. Daily caloric need varies by age, sex, height, and physical activity levels. ### Chemical Energy Powering the Body Refer to [*Mitochondria*](#mitochondria). Nutrients inside cells can be oxidized via cellular respiration to generate energy in the form of ATP. Fat is very valuable as an energy source, more than carbohydrates or proteins. ### Undernourishment, Malnourishment, and Essential Nutrients **[Undernourishment]** is when you have a deficiency in calories. **[Malnourishment]** is when you have a deficiency in one or more essential nutrients. An **[Essential Nutrient]** is a material that must be supplied to you via your diet. Your body cannot fabricate them. There are four classes of essential nutrients: - Essential Fatty Acids - Essential Amino Acids - Minerals - Vitamins ### Macronutrients There are three types of macronutrients: - Carbohydrates - Proteins - Lipids ### Fibre Fibre consists of indigestible carbohydrates. There are two main ways of categorizing fiber types: - From the foods that fibre comes from - Solubility or insolubility Fibre normalizes bowel movements and maintains bowel health. It decreases risk of constipation, diverticular disease (occurs when small, bulging sacs or pouches form on the inner wall of the intestine), and colon cancer. Fibre also lowers cholesterol levels (Fibre does this by binding to cholesterol as it passes through your digestion), blood pressure (by doing the former), and inflammation, therefore, it also decreases the risk of heart disease. Fiber also helps control blood sugar vessels by slowing the absorption of sugar, thereby decreasing risks of Type II diabetes. Fibre also aids in achieving a healthy weight -- foods rich in fibre are more filling and less energy-dense. ### The Glycemic Index The Glycemic Index measures how fast and how far blood sugar levels will rise after eating carbohydrates. High GI-level foods are digested quickly and converted to blood sugar immediately, causing blood sugar levels to spike. Low GI-level foods are digested more slowly, causing a slower rise in blood sugar levels. A diagram of food items Description automatically generated\ The risk with over-ingesting High GI-Level foods is that your cells will get used to the insulin response, thus, type II diabetes. ### Review Of Proteins Proteins are composed of Hydrogen, Carbon, Nitrogen, and Oxygen. They're relatively large molecules made of amino acids joined by peptide bonds. They form hormones, enzymes, and antibodies, help the body regulate fluids and electrolytes, buffer pH, and transport nutrients. ### Amino Acids There are 20 Standard Amino Acids used by cells in making proteins. Our bodies can synthesize 12, but there are 8 that we must get from our diets (This is possible for both carnivorous and vegetarian diets, with the right combination of plant foods.) There are 9 Essential Amino Acids you need in your diet. 11 are non-essential. The body requires amino acids to produce new proteins and replace damaged ones. ### Review of Lipids Composed of Carbon, Hydrogen, and Oxygen. They store energy, protect organs, and regulate temperatures. #### Types of Lipids ##### Triglycerides Composed of 3 fatty acids and one glycerol molecule. ##### Saturated Fatty Acids A Fatty acid with carbon chains fully saturated with hydrogen. ##### Monounsaturated Fatty Acids ##### Polyunsaturated Fatty Acids #### Essential Fatty Acids Essential Fatty Acids are required for good health, but the body cannot fabricate them, so we need to ingest them. There are two fatty acids known to be essential for humans: Alpha-linoleic (Omega-III fatty acid used to make phospholipids of cell membranes and are converted to other important molecules, like anti-inflammatory molecules) and Linoleic (Omega-VI fatty acid like alpha-linoleic, but pro-inflammatory molecules) There are others that the body *can make*, but we'll have less than enough if we rely on bodily production. Eicosapentaenoic Acid (EPA for your sanity) is an Omega-III fatty acid and an important antioxidant, obtained via fish oil or oily fish. Docosahexaenoic Acid (DHA) (Omega-III) is an important structural component of the brain, skin, retina, sperm, and testicles, found in fish oil and breastmilk. ### What even *is* an Omega-III/VI Polyunsaturated fatty acid, anyway? Polyunsaturated fatty acids (PUFAs) have two or more double bonds. There are two types of PUFAs in dietary oils: Omega-III and Omega-VI. They're distinguished by the position of the first double bond. #### Balancing Omega-III and Omega-VI Omega-III and Omega-VI fatty acids are both important for health, but they have opposite effects on our inflammatory response. Ideally, we should have more Omega-III and less Omega-VI fatty acids in our diets. ### Major and Minor Dietary Elements There are several inorganic elements essential to bodily function. Humans need 7 major dietary elements: Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, and Magnesium. You need more than 200 mg/day of all of these. Other micronutrients, we need less than 100mg/day of, such as Iron, Cobalt, Chromium, Copper, Iodine, Manganese, Selenium, Zinc, and Molybdenum. #### Functions of Dietary Elements Ions are found in blood plasma and cell cytoplasmic composition (like sodium, potassium, and chloride). Minerals represent much of the chemical composition of bones (calcium, phosphorus). Ions contribute to nerve and muscle activity, such as sodium, potassium, and calcium. ### Mineral Requirements ***SFAT -- Mostly Mineral and Function*** ### Vitamins Vitamins are organic compounds (carbon and hydrogen covalently bonded) that are essential for proper body function but are required in small amounts. Vitamins are mostly obtained via food, because the body is unable to fabricate the survival-necessary ones. Severe problems can result if the diet is deficient in these vitamins, or if they are consumed in excess. Vitamins are either fat soluble (nonpolar) or water soluble (polar). ***SFAT: Vitamin B9 (Folic Acid) and Vitamin C*** #### More on Folic Acid Folic acid decreases the risks of birth defects and cancer. It's required in the first four weeks of pregnancy (embryogenesis) for expecting mothers, for the brain, skull, and spinal cord to develop properly. It prevents spina bifida and neural tube defects. The current recommended intake for folic acid is 400mg/day, and people who get more than the recommended amount have a lower risk of colon or breast cancer. Folic acid is in our diet through dark green vegetables, dried legumes, and in Canada, folic acid is added to all white flour, enriched pasta, and cornmeal products. Having too much folic acid isn't a problem because it's water soluble. It'll exit through the digestive system if there's too much of it. This isn't true for, however... #### Fat Soluble Vitamins To absorb these vitamins (Vitamins A, D, E, and K), you need fat in your diet. You cannot excrete them. Dietary Fat -\> Bile Secretion -\> Vitamin Absorption They're stored in fatty organs such as the liver, spleen, and adipose tissue. Excessive amounts of them can accumulate and result in toxicity. This typically won't happen, however, unless you abuse supplements. #### More on Vitamin D Vitamin D supplement abuse is prevalent on the West Coast (for obvious reasons) because of the misconception that it prevents "winter depression". The resulting excess Vitamin D creates stiffness in bones and organ tissues (which is an alarming thing for obvious reasons). Low vitamin D, on the other hand, leads to higher risk of various forms of cancer, and the strongest evidence links Vitamin D-ficiency (bad joke, I know) to increased risk of colorectal cancer. Vitamin D is acquired via sunshine, fatty fish, fish liver oil, eggs, and dietary supplements.\ Foods in our diet are fortified with Vitamin D such as milk, juices, and breakfast cereals. ### Water We know already -- water is the main component of our bodies (60% of our bodily weight). It is our body's universal solvent. ### Food Labels Recall from BIOL 1111 Lab \#4: Food labels provide important nutritional information about packaged foods. Ingredients are listed from greatest to least amounts. Chances are that weird chemicals on your labels (like Calcium Sulfate) are preservatives. Nutrition facts include serving sizes, calories/serving, and the amount of selected nutrients per serving and as a percentage of daily value based on a 2000cal/day diet. ### So, How Do We Know All This Stuff About Nutrition, Anyway? Epidemiology. Basically, we use statistics from populations to work out the dynamics of how different parts of our diet affect different parts of our bodies. For example, prior to '98, significantly more babies were born with spina bifida. Epidemiologists discovered that women of low socioeconomic status delivered more babies with spina bifida due to low folic acid in their diets. ### Pretty Good Foods Turmeric and Acai berries are pretty good for you, but remember that their benefits are *kiiiinda* overhyped, so take them with a pinch of salt. ### Obesity as a Health Problem ***Overnourishment*** is what happens when more food energy than is needed for normal metabolism is ingested. Obesity is the excessive accumulation of fat that has a negative impact on health. It is a global health problem that now surpasses smoking in its contribution to disease and the shortening of healthy lifespans. In the U.S, the obese percentage of the population has double to more than 30% in the past two decades, and another 35% are overweight (65%!) Obesity leads to Type II diabetes, breast and colon cancer, and cardiovascular disease. #### Leptin's Fault? Leptin is a hormone that is produced by adipose (fat) cells that suppresses appetite. As adipose cells increase in size, leptin levels increase, and the brain suppresses appetite. In some people, a defective leptin gene leads to obesity, and synthetic leptin may help some people with this condition. #### What causes obesity in people? A combination of factors such as a lack of exercise, poor eating habits, genetic factors, and endocrinal abnormalities (including too little thyroid hormone, too much cortisol, or too little growth hormone) ### So, What Even ***Is*** the Best Diet Out There, Anyway? Inconclusive. Here are, however, some of the more popular ones out there: - The Intermittent Fasting Diet: 5 days normal, 2 days fasting - The Dukan Diet: Low-Carb, High-Protein diet - The Paleo Diet: The hunter-gatherer diet: no agriculture, no processed foods). - The Atkins Diet: No carbs and lots of protein, where fat is OK. Contains red meat, butter, cream, cheese, and mayonnaise... - The Alkaline Diet: The idea is that modern diets cause our body to produce too much acid, which becomes fat (this is verifiably false by what we know about acids and fats in BIOL 1111). The idea is to cut down on meat, sugar, and alcohol, and substitute with more fruits and veggies. - The Tapeworm Diet....?: Infect yourself with a parasitic tapeworm larva that absorbs the excess calories you eat; therefore, you don't gain any weight. (Seriously, how down bad do you have to be to shell out \$10,000 for this crap?!) Seven words to sum up a good diet: "Eat food. Not too much. Mostly plants." ### The Importance of Physical Activity It's important to your health. Physical activity reduces anxiety and stress, improves fitness, confidence and self-esteem, and promotes the maintenance of a healthy weight. Scientific research strongly supports the role of physical activity in disease prevention, especially chronically disabling conditions such as: - Cardiovascular disease - Cancer - Diabetes - Osteoporosis - Arthritis - and Obesity. Ideally, you want to engage in 3 different types of physical activity to keep healthy: #### Endurance Activities Endurance-based activities help your heart, lungs, and circulatory systems stay healthy and give you more energy. #### Flexibility Activities Flexibility activities help you to move easy, keep your muscles relaxed, and your joints mobile. #### Strength Activities Strength activities help your muscle and bone stay strong, improve your posture, and help to prevent diseases like osteoporosis. The Human Digestive System -------------------------- Remember how, earlier on in BIOL 1111, we talked about how we would progress from atoms to single cells to tissues to organs to organ systems? Now, we'll be talking about your ever-important *Human Digestion System.* ### Why do We Eat? We eat because we need to ingest energy and building blocks for regulating our bodies. Remember all those nutrients we couldn't make ourselves? Primarily, for those. ### Types of Feeders For life, there are more ways of consuming things outside of itself than just eating. Absorptive feeders lack a digestive tract or a mouth; instead, they absorb through their body surfaces, like the Tapeworm. Ingestive feeders eat through a mouth and digest through a system. Three types of ingestive feeders; herbivores, carnivores, and omnivores. ### The Four Stages of Food Processing First, ingestion is, well, the act of eating. You pop something in your mouth and down the hatch. Digestion happens when you break down the food into molecules small enough for step three, Absorption, where you take up the products of digestion, through the cells that line your digestive tract, and lastly, four, Elimination, where non-absorbable materials exit through the digestive tract. ### The Alimentary Canal The alimentary canal is a tube running from mouth-to-anus. This tube is divided into specialized regions for every specific function your digestive tract needs to carry out. The main parts of the human alimentary canal are the: - mouth - oral cavity - tongue - pharynx - esophagus - stomach - intestines - rectum - anus In addition to your canal, there are *accessory tissues* such as your salivary glands, your gallbladder, your pancreas, and your liver. ### Functions of the Digestive System The digestive system has four main functions: - Motility - The movement of materials through the GI tract through ingestion, chewing, the pushing into the pharynx by the tongue, and peristalsis (rhythmic smooth muscle contractions). - Secretion - Includes exocrine (digestive enzymes, bicarbonate, HCl) and endocrine (hormones that regulate digestion) secretions - Digestion - There are two phases of this one: Mechanical (your chewing, your stomach movements) and Chemical (enzyme-aided reactions, etc.) - Absorption - The passage of your digested food molecules into the blood or lymphatic system. ### Exocrine-Endocrine Aside and Hormones An exocrine substance is a substance released into a series of ducts and open spaces, never into the bloodstream. ***A hormone is defined as any substance released by cells into the bloodstream to a targeted destination.*** ### The Oral Cavity The teeth break up your food. There are four types of teeth: - **Incisors** for the initial bite, - **Canines** for tearing, - **Premolars** and **Molars** for grinding and crushing. Based on this pattern, we are omnivores, because our teeth can handle both meat and plants. Our salivary glands produce saliva. Saliva moistens and lubricates food for passage. The buffers within our saliva neutralize acids, the antimicrobial agents kill microbes (of which, there's also one in our tears to kill bacteria in our eyes), and the ***salivary amylase*** within it begins starch hydrolysis. Lastly, the tongue pushes the chewed food (bolus) into the pharynx. ### Past the Pharynx The swallowing reflex moves food from the pharynx into the esophagus. The epiglottis is a tissue flap that prevents food from going down the wrong pipe, your *trachea*. Your ***upper esophageal sphincter*** regulates the opening of the esophagus. ### Peristalsis and the Stomach In the esophagus, a process called peristalsis, which is rhythmical muscle movement, moves the food bolus down into the stomach. Your ***lower esophageal sphincter*** regulates the passage of food through the esophagus and into the stomach. The stomach, capable of storing 2L of food and drink, sits just under the diaphragm, and conducts storage, plus mechanical and chemical digestion. The stomach also secretes gastric juices, which are made up of: - Mucus, that prevents the other two juices from wreaking havoc in your cell lining - Pepsin, an enzyme in the stomach that breaks down proteins - Strong acid. Your stomach is ***incredibly acidic*** (pH of 2 or 3). It kills ingested bacteria, breaks apart food cells, and denatures proteins. The stomach churns food with gastric juice to form a mixture known as acid chyme. The stomach is closed at either ends by the cardiac (at the top) and the pyloric (at the bottom) sphincters. The pyloric sphincter opens to allow the passage of acid chyme into the small intestine. Heartburn, which of course doesn't appear in the heart, occurs when your acid chyme moves up your cardiac sphincter and moves into your esophagus, which your esophageal lining was ***never*** meant to handle. It's relieved typically by taking antacids. ### Gastric Ulcers Gastric ulcers, open sores in the stomach lining, can lead to diverticulitis and are typically caused by a spiral-shaped prokaryote called *H. pylori*. They erode your protective mucus and allow the acid chyme to break down the stomach lining. ### The Small Intestine The small intestine is the major organ of chemical digestion and nutrient absorption. You have two glands that empty into the small intestine and aid in digestion: #### The Pancreas The pancreas produces digestive enzymes and an alkaline solution that neutralizes the acid chyme. #### The Liver The liver produces bile which is stored in the gallbladder. This bile emulsifies fat droplets so they can be dissolved by pancreatic enzymes. #### Chemical Digestion Small-intestine wall enzymes complete the digestion of many different nutrients. #### The Three Regions of the Small Intestine The Duodenum is the shortest segment of your small intestine, 25cm long. It begins at the pyloric sphincter and merges with the Jejunum, mixing contents and secretions from the pancreas and liver. The Jejunum is 1 meter long, and aides in chemical digestion and absorption. The Ileum is about 2 meters long and joins the large intestine to the ***ileocecal sphincter.*** Its function is to absorb nutrients. #### The Surface Area of the Small Intestine The small intestine has a large surface area to aid in nutrient absorption. Folds of the intestinal lining, villi, have folds on them called microvilli that contribute to the large internal surface area. Nutrients pass into the epithelial (adjective: denoting the thin tissue lining the alimentary canal and other hollow structures) cells of the villi. Fatty acids and glycerol are recombined into fats and transported into the lymphatic system. #### Circulation Blood travels from the intestines to the liver via the hepatic portal vein. The liver also stores nutrients (such as glycogen), detoxifies toxic substances, and converts nutrients to other substances the body can use. ### The Large Intestine 1.5 meters long, also known as the colon. Anything not digested goes here. Water is absorbed by the colon. Microbes that live in this region are essential for producing vitamins such as Vitamin K, Folic Acid and B-vitamins. We give them a comfortable living environment, and they help us create these vitamins for bodily use in return. Feces is produced and compacted by the colon. This feces consists mainly of undigested material, such as fibre and cellulose. ### The Rectum The rectum stores feces until it can be eliminated. There are two sphincters that the rectum consists of. The first sphincter opens from the large intestine to the rectum and is involuntary. The other sphincter opens up into the anus and is voluntary. ### Side Note on Diarrhea and Constipation Diarrhea happens when your gut can't absorb any nutrients, and the speed of passage is rapid and watery as a result. Constipation is the opposite. Too much water is absorbed, and the speed of passage is sluggish and dry as a result. This brings us to the end of [***Nutrition***.] Are we good to go? Good. Now is probably the time to lock in and work a little bit harder going forward to knock your second midterm and final exam out of the park. The Unifying Concepts of Animal Structure and Function ====================================================== Overview -------- In *The Unifying Concepts of Animal Structure and Function,* we'll be discussing tissues, organs, and how organ systems work together to maintain and regulate the body. In Biology, there's a recurring theme composing hierarchical organization and the correlation between structure and function. Levels of Organization ---------------------- ### Human Development From zygote to newborn, there are 41 mitotic divisions (2^41^), creating \~2.2 trillion cells. A lot of cell differentiation takes place in this stage, where cells specialize in the bodily function they'll be serving throughout their lifetime. ### The Human Body In the study of the human body, ***anatomy*** is known as the study of structure and relationships among structures. ***Physiology*** is the study of how bodily structures function. ### Form and Function Never forget this, as it's a commonly recurring theme in BIOL 1111: ***In the study of living things, the form of something goes a long way to explaining what it does.*** An organism's phenotype is the expression of its genotype. An important concept in biology is that Natural Selection is **editing** rather than **creating.** Tissues ------- A tissue is an integrated group of cells that all perform a specific function. Tissues are made of cells, junctions, and extracellular material. We have four different types of tissues: ### Epithelial Tissue ***SFAT*** Epithelial tissues cover body surfaces and internal organs/cavities. Some examples of this tissue include the epidermis and the stomach lining. Cells are riveted together by watertight junctions. Epithelial tissues have nerves, but no blood vessels. They also always have a free surface exposed to air or fluid. They function as a barrier to mechanical injury, invasion by microbes, and fluid loss. Some are specialized to facilitate absorption or secretion roles. All glands are composed of epithelial tissue. As is with *Form and Function*, you can get a clue as to what an epithelial tissue does based on what it looks like. ### Connective Tissue Connective tissues are characterized by sparse cells. The cells manufacture and secrete extracellular matrices composed of fibres embedded in liquids, solids, and gels. Connective tissues make up the basic support structures of the body and connect the body's other tissues in a manageable framework. They hold organs in place and attach epithelia to underlying tissues. #### Loose Connective Tissue Loose connective tissues are loose weaves of fibres that serve as binding and packing material holding other tissues and organs in place. #### Fibrous Connective Tissue Fibrous connective tissues are dense due to an arrangement of a large number of collagen fibres in parallel bundles, which serve to impart tensile strength. They're found in tendons and ligaments. #### Adipose Tissue Adipose tissue stores fat. It also stores energy and is good for insulation. Each fat cell contains a single large fat droplet for future use. #### Cartilage Tissue Cartilage is composed of collagen fibres embedded in a rubbery matrix. It comprises the skeleton of every vertebrate embryo. In most vertebrates, it's eventually replaced with bone. Cartilage, like fibrous connective tissue (think, your ACL), isn't vascularized well, therefore, does not heal very well. #### Bone Tissue Bone tissue provides support and protection for the vertebrate body and its organs. It's a matrix of collagen fibres embedded in calcium salts. Bones are vascularized, therefore, heal in six weeks as opposed to the eight months taken by cartilage and FCT. #### Blood This is a little weird to think about, but blood is also technically a connective tissue. It's a liquid extracellular matrix of plasma, containing water, salts, and proteins. ### Muscle Tissue Muscle tissue is the most abundant tissue in most animals. It consists of long, excitable cells capable of contraction. Muscle tissues control body movement. Posture, respiration, organ constriction, your heartbeat, and your bodily heat production are controlled by muscle tissue. All muscle tissue has four specific properties: Contractility (the ability to shorten with force), excitability (responsiveness to stimuli), extensibility (the ability to stretch beyond normal resting length), and elasticity (the ability to return to resting length if stretched). There are three types of muscle tissue: Skeletal, Cardiac, and Smooth muscle tissue. ### Nervous Tissue Nervous tissue senses stimuli and rapidly transmits signals from one part of the animal to another. It coordinates and controls bodily activity. The major cells of nervous tissue are called neurons. Neurons carry signals by conducting electrical impulses. Recall from PSYC 1115's [*Neural Communication*](../PSYC%201115%20-%20Intro%20to%20Biological,%20Cognitive,%20and%20Developmental%20Psychology%20-%20PSYC_V%20100/PSYC%201115.docx): Neurons are composed of a nucleus, dendrites, and axons, protected by myelin sheaths. Organs and Organ Systems ------------------------ Tissues organize (no pun intended) to form organs. Each organ is made of several tissues that cooperate to perform specific functions. Most organs have tissues layered in arrangement. For example, the heart has extensive muscle that generates contraction, epithelial tissue that lines the heart chambers, connective tissues that make the heart elastic, and neurons that regulate contractions. ### The Body as a Cooperative of Organ Systems Organs may be organized into organ systems, which consist of several organs with separate functions that act in a coordinated manner. These systems are interdependent. They work together to perform the functions of their host *organism*, a living whole greater than the sum of its parts. There are 12 major organ systems in animals. ***SFAT*** ***Integumentary, Skeletal, Muscular, Nervous, Endocrine, Cardiovascular/Circulatory, Lymphatic, Immune, Respiratory, Digestive, Reproductive, and Urinary/Excretory.*** ***Call each X/Y either X or Y. Don't write both on a test.*** #### The Digestive System Refer to [*The Human Digestive System*.](#the-human-digestive-system) It ingests and digests food and absorbs its nutrients into the bloodstream while excreting out waste. #### The Respiratory System The respiratory system exchanges gases with the environment. It supplies the body with oxygen and disposes of carbon dioxide. It's composed of the pharynx, larynx, trachea (do ***not*** call this your windpipe), bronchi, and lungs. #### The Cardiovascular System and the Artery-Vein Difference The cardiovascular system is primarily composed of your heart and your blood vessels. Keep in mind, in anatomical models, ***arteries*** (this does ***not*** have anything to do with oxygenation) are ***red*** and carry blood away from the heart, and ***veins*** carry blood to the heart and are colored ***blue***. #### The Urinary System The Urinary System removes waste products that are produced via cellular metabolism. It's composed of your kidneys, ureters, urinary bladder, and the urethra. The urinary system also regulates the water balance of blood. #### The Muscular and Skeletal Systems The muscular and skeletal systems support and move the body. The skeletal system provides the body structural support, while the skeletal muscles move parts of the body because they are attached to bone and cartilage. #### The Integumentary System Basically, your skin, hair, and nails. It protects the body from mechanical injury. Your skin is composed of multiple layers designed to protect the inner body from foreign organisms. #### The Lymphatic System (*In anatomical models, **green** is always the lymphatic system, but it also sometimes might be yellow).* The lymphatic system supplements circulation by filtering body fluids. The immune system works with the lymphatic system, specifically the lymph nodes, to protect the body. The lymph nodes are typically a chilling space for white blood cells when they're off the job due to a lack of infection.\ *(side note: now might be a good time for a rewatch of both editions of Cells at Work!)* Your lymphatic system is composed of your lymph nodes, appendix, thymus, spleen, bone marrow, and lymphatic vessels. #### The Nervous and Endocrine System These two go hand-in-hand. Your nervous system is composed of your brain, sense organs (your ear), spinal cord, and nerves. The endocrine system is composed of the thymus, hypothalamus, pituitary gland, thyroid gland, pancreas, adrenal gland, parathyroid gland, and the (testes/ovaries). #### The Reproduction System The reproduction system makes more of an organism. In females, the reproduction system is composed of the ovaries, uterus, vagina, and oviducts. In males, the reproduction system is composed of seminal vesicles, prostate glands, [vas deferens,](https://en.wikipedia.org/wiki/Vas_deferens) the penis, the urethra, and the testes. External Exchange/Internal Regulation ------------------------------------- ### Homeostasis The body needs to maintain homeostasis -- that is, the state in which the body maintains a temperature, pH and salt concentration-stable environment. ### Thermoregulation Humans and mammals in general are called ***endotherms*** because we use internal metabolic heat to thermoregulate. Contrast with lizards and snakes, who cannot internally generate enough heat to maintain their body temperature, and are called ***ectotherms***, because they need to stay in environments that help them prop up their internal temperature. Through thermoregulation, our body is kept at 37.7C via the use of ***feedback loops***. ### The Negative Feedback Loop The hypothalamus is a structure right above the brain stem in the base of the brain. It acts as the body's automatic thermostat. It receives signals from many different sensor cells that detect sensory input in the body and sends signals to ***effector cells*** that affect the state of the body. A feedback loop is a pathway that involves sensory input, a response via an effector, and the detection of a response via sensor. ***SFAT*** the following diagram. Understand it well. The output of a circuit inhibits the input of the circuit, thereby helping the system reach its set point, ***homeostasis***. Think of those Boston Dynamics robots adjusting their posture in response to a sense of non-equilibrium for an analogy. #### What if you're too cold? To conserve heat, your body will perform peripheral vasoconstriction, where blood sent to the extremities is decreased (in extreme conditions, to the point of frostbite) to conserve bodily heat. It will also shiver in order to generate heat via contraction. #### What if you're too hot? Your body will perform peripheral vasodilation, where the body sends more blood to the extremities to expel heat. Sweating cools the body via releasing heat to the air. ### Positive Feedback loops The opposite, where an output of the system becomes a stepping stone to a larger response from the system. ### Blood-Glucose Homeostasis Glycemic (Glycemia: glyc- : sugar, -emia: blood) levels must be maintained at 80-120 mg/mL of blood. ### Osmoregulation See *[Osmoregulation](#osmoregulation)* under *Cell Function*. Osmolarity is the concentration of dissolved solutes in blood. Among the solutes dissolved in blood are electrolytes -- sodium, potassium, etc. Our body maintains 300 mOsm (milliosmoles) via osmoregulation. If the hypothalamus registers a higher-than-normal solute concentration in our blood, it will trigger a sense of thirst, as well as triggering the release of ADH (antidiuretic hormone) from the pituitary gland, traveling through the bloodstream and acting on kidneys. ADH signals the kidneys to excrete less water in urine, and instead reabsorb it into the bloodstream. Water in the bloodstream further dilutes the solute concentration. ***This slide right here is the cutoff for Midterm 2. Get going. It's in a little over a week.*** The Vascular System =================== The Flow of Blood Throughout the Body ------------------------------------- Imagine, for a minute, you are a red blood cell. For the sake of our course, blood starts out in the right ventricle of the heart, deoxygenated. When the heart contracts, blood can only go in one direction,

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