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General Biology Chapter 1-2.3 Notes

by: Jamie Wieder

General Biology Chapter 1-2.3 Notes 1005

Marketplace > Virginia Polytechnic Institute and State University > Biology > 1005 > General Biology Chapter 1 2 3 Notes
Jamie Wieder
Virginia Tech

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These notes go over the fundamentals of biology, atomic structure, types of bonds, scientific method, macromolecules and their structure...
General Biology
MV lipscomb
Class Notes
Biology, carbon bonds, hydrogen bonds, ionic bonds, covalent bonds, Macromolecules, cells, scientific theory
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This 15 page Class Notes was uploaded by Jamie Wieder on Thursday September 1, 2016. The Class Notes belongs to 1005 at Virginia Polytechnic Institute and State University taught by MV lipscomb in Fall 2016. Since its upload, it has received 45 views. For similar materials see General Biology in Biology at Virginia Polytechnic Institute and State University.


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Date Created: 09/01/16
Tuesday, August 23, 2016 Lesson One Lesson One Textbook Notes Intro: The first organisms on the Earth were not plants or animals or humans like we know today. Plants and animals like we know today have only existed for the last 130-200 million years and humans only the last 200,000. So what is biology? Biology is the study of life. All groups of organisms have characteristics/functions that make them living 1. order 2. sensitivity or response to stimuli 3. reproduction 4. adaptation 5. growth and development 6. homeostasis 7. energy processing Order Organisms are made up of one or more cells and each cell has atoms that make up molecules. Multicellular organisms which are made up of millions of individual cells, have an advantage bc their cells are specialized to preform special functions. Sensitivity or Response to Stimuli Organisms respond to all sorts of stimuli. 1 Tuesday, August 23, 2016 EX. Lights “lean” towards the sun In addition to this, bacteria can move away or towards chemicals. Movement towards a stimuli is considered a positive response Movement away from a stimuli is considered a negative response. Reproduction Single cell organisms reproduce by duplicating their DNA and dividing it equally when the cell divides into two cells. Multicellular organisms often produce reproductive cells that form new individuals. When this happens, DNA containing genes is passed along to the offspring. Growth and Development Organisms grow and develop according to the instructions from their genes. These instructions direct cellular growth and development and ensure that the young will have some of the same characteristics as their parent. Regulation All organisms require multiple regulatory mechanisms to coordinate internal functions like moving nutrients, responding to stimuli, and dealing with environmental stress. EX organ systems in the human body with specific jobs like circulatory systems and digestive system. Homeostasis Cells must have certain conditions like temperature, pH, and concentrations of chemicals to be able to function. These needs may change, however. Organisms are able to maintain their internal conditions constantly with a process called homeostasis. EX Many organisms can maintain their body temperature with thermoregulation like the polar bear with have bodies that help them withstand the low temperatures. EX Thermoregulation is also when humans sweat when they are hot. Energy Processing All organisms use a source of energy for their activities. 2 Tuesday, August 23, 2016 Some organisms capture energy from the Sun and use it for food where as others use chemical energy from molecules they take in. Levels of Organization of Living Things Organisms are organized on a hierarchy from small to large. • An atom is the smallest unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules which are chemical structures consisting of at least two atoms held together by a chemical bond. • Many molecules that are biologically important are macromolecules - large molecules that are typically formed by combining smaller units called monomers. EX of macromolecules is DNA • Some cells contain aggregates of macromolecules surrounded by membranes which are called organelles. Organelles exist inside of cells and preform specialized functions. • Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single celled organisms that lack organelles surrounded by a membrane and do not have a nuclei surrounded by a nuclear membrane. Eukaryotes do have membrane bound organelles and nuclei. • Most multicellular organisms combine to make tissues which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present in animals and plants. Organisms are individual living entities. All individual species living within a specific area are called a population. When many • different plants or species live in a specific area, that is called a microbial population. • A community is the set of populations inhabiting a particular area. • An ecosystem consists of all the living things in a particular area including nonliving things. • The highest level is the biosphere which is a collection of all of the ecosystems which includes water, land, and atmosphere. Diversity of Life The source of the diversity on Earth is evolution - the process of gradual change during which new species arise from older species. In the 18th century Carl Linnaeus first proposed organizing the known species of organisms into a hierarchal taxonomy. In this system, species with similar traits are put 3 Tuesday, August 23, 2016 together in groups called genus. Further genera (groups of genus) are put together in a family. This continues until all the groups are together at the highest form. • There are currently eight levels of hierarchy - species, genus, family, order, class, phylum, kingdom, domain The highest level, domain, is a new addition to the system since the 1990’s. There are three domains of life - Eukarya, Archea, and Bacteria. • Eukarya contains organisms that have a nuclei with the kingdoms fungi, plants, animals , and several protists. • The Archea are single celled organisms without nuclei that live in harsh environments The Bacteria are different single celled organisms that do not have a nuclei • Linnaeus was also the first to name organisms based on the two unique names - binomial naming system. Binomial names consist of genus name (which is capitalized) and the species name (which is lowercased). Both names are italicized when written. Branches of Biological Study -Molecular biology is at the molecular level - interactions between DNA and RNA and proteins and the way they are regulated. -Mircobiology is the study of the structure and function of microorganisms. -Neurobiology studies the nervous system and is also known as neuroscience. -Palentology studies fossils to know the history of life -Zoology and botany are the study of plants and animals -Ecologists study the interactions between organisms and their environment -Physiologists study the workings of cells, tissues, and organs The Nature of Science What is science? Science is a study of the natural world. Historically, science is responsible for technological revolutions The scientific method is a method of research with defined steps that include experiments and observation. One of the most important aspects of the scientific method is testing a hypothesis. A hypothesis is a suggested explanation for an event that can be tested. These are generally produced within the scientific theory which is a 4 Tuesday, August 23, 2016 generally accepted and tested explanations for a set of observations. There are also elements that are scientific laws which are expressed in mathematical formulas which explain how the environment will react under certain conditions. Scientific Inquiry One thing common to all sciences is the goal to know. And to do this we use inductive and deductive reasoning. Inductive reasoning is a form of logical thinking that led related observations to arrive at a conclusion. This kind of data can be quantitative or qualitative. From these we can often conclude. Deductive reasoning is a type of logic used with hypothesis based science in which you use a general principle or law to forecast a result. From this a scientist can predict a result as long as the principle is valid. Descriptive science aims to observe and explore and discover Hypothesis based science begins with a specific question or problem and a potential solution that can be tested. Hypothesis Testing The first time the scientific method was documented was by Sir Francis Bacon in 16th century who set up inductive methods for scientific inquiry. A hypothesis must be testable to ensure that it is valid and falsifiable - can be disproven by experimental results. To test a hypothesis, scientists must conduct one or more experiments to eliminate or disprove a hypothesis. Each experiment will have one or more variables and one or more controls. Remember that rejecting one hypothesis does not mean that all other hypotheses are valid. In practice the scientific method is not rigid and linear but instead it leads to more questions and brings new pieces to the puzzle. Basic and Applied Science Basic science (“pure science”) seeks to expand knowledge regardless of the short-term application of the knowledge. It is knowledge for he sake of learning - without a big value. 5 Tuesday, August 23, 2016 Applied Science (“technology”) aims to use science to solve real world problems and makes it possible to make improvements. 6 Tuesday, August 23, 2016 Lesson Two Lesson Two Textbook Notes Intro The elements carbon, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form carbs, nucleic acids, proteins, and lipids that are fundamental molecular components of all organisms. Food provides an organism with nutrients- the matter it needs to survive. Many of these critical nutrients come in the form of biological macromolecules necessary for life. Matter take sup space and had mass and us composed of elements that can not be broken down. Atoms No single atom can be broken down into anything smaller without losing the properties that make it hydrogen. All atoms are made of protons, electrons, and neutrons. Proton is positive and lives inside the nucleus with a mass of 1 and a charge of +1. An electron has a negative charge and travels around the outside of the nucleus and has a charge of -1. Neutrons reside inside the nucleus and have a mass of 1 but no charge. Protons and electrons balance each other out to have a net zero charge for neutral atoms. Different elements have different melting and boiling points and combine in different ways. Chemical Bonds Atoms are their most stable when they have their outermost shells filled. To achieve complete stability atoms will share, give, or donate electrons to other atoms. Because of the openings in the shells there are the formation of chemical bonds. 1 Tuesday, August 23, 2016 When am atom does not contain the same number of protons and electrons it is known as an ion. Positive ions are known as cations and negative ions are called anions. The movement of electrons from one element to another is known as an electron transfer. Ion Bonds Ionic bonds are when there is a positive and negative ion that share the extra electron to become balanced and form a type of grid formation. These types of bonds are very strong and require a lot of energy to pull apart. Covalent Bonds Covalent bonds are strong between two or more atoms. These bonds are formed when there is electrons shared between the purest form of elements in nature that make up biological molecules. Covalent bonds do not dissociate in water unlike ionic bonds. EX hydrogen and oxygen forming together to make water There are two types of covalent bonds : non polar and polar bonds. Non polar bonds form between two atoms of the same element or different elements that share electrons equally. Polar covalent bonds are formed when shared electrons spend time closer to one nucleus than the other and a slightly positive or negative charge is formed. Hydrogen Bonds These are attractions between positive and negative charges that do not take much energy to break apart. When a hydrogen polar covalent bond is formed, the shared electron is pulled farther away from the hydrogen nucleus and therefore makes the hydrogen atom slightly positive. This will slightly attract neighboring negative atoms to form a weak bond called a hydrogen bond. Hydrogen bonds can form between atoms that do not include a water molecule and are responsible for some three dimensional structure of proteins. 2 Tuesday, August 23, 2016 Van der Waals Interactions These are also weak attractions between molecules. they occur between polar covalent bound atoms of different molecules. These can be caused by temporary charges as the electrons move around the nucleus. Water In a water molecule, the electrons shares spend more time with the oxygen atom then with the hydrogen tom. Although there is no charge to a water molecule, the positive hydrogen and slightly negative oxygen, because of this the hydrogen atoms repel each other and make a unique shape. Water molecules attract other water molecules and form hydrogen bonds. When a substance forms hydrogen bonds with water, it can dissolve in water and is known and hydrophilic. Hydrogen bonds that are not readily formed with non polar substances and are known as hydrophobic bc they don't dissolve in water. Water absorbs a lot of energy before its temperature rises and therefore water moderates temperature within organisms in their enviornments. As energy input continues the balance of formation and destruction of bonds is more destructive and results in the release of water molecules at the surface of the liquid and this is evaporation. Evaporation is like sweat and allowed for cooling of an organism bc the breaking of hydrogen bonds uses a lot of energy and needs cooling. As molecular motion decreases and temp drops, there is less energy and a rigid form is bond - like ice. Because water is polar ir can readily dissolve other substances and known as a solvent. The charged particles will create a circle called the sphere of hydration around the particle to separate it. These are known as hydration cells. Water is very cohesive because water molecules are attracted to each other keeping the molecules together. Cohesion gives the rise of surface tension - how much a substance can withstand pressure under stress. These forces relate to the property of adhesion in water molecules to other molecules. 3 Tuesday, August 23, 2016 Buffers, pH, Acids, and Bases What is pH? It is the measure of acidity. The overall concentration of hydrogen ions yield a low pH and with fewer hydrogen ions the pH is higher. It is inverse. Pure water is neutral, neither acidic nor basic. Acids have higher levels of hydrogen ions and a lower pH and bases have lower levels of hydrogen and higher pH. The stronger the acid, the more it donates its H+. Our bodies function between 7.2 and 7.6 pH and if it is outside the range, the breathing system wont work. Buffers are what absorb the excess H+ and OH- to make sure the body is regulated. An example of a buffer is carbon dioxide. 4 Sunday, August 28, 2016 Chapter 2.3 Notes Bio 1005 Macromolecules The large molecules that are needed for life are made up of smaller molecules called macromolecules. These macromolecules make up most of the mass of the cell and preform many different functions. They are organic and contain carbon and other minor elements. There are four types of macromolecules. 1. proteins lipids 2. 3. carbohydrates 4. nucleic acids Lets talk about Carbon Earth is “carbon-based” and this means that carbon atoms bond to other carbon atoms and most other elements and this makes up the molecules in almost all living things. It is the foundation of life. Carbon has four electrons in its outer shell which means it can form four covalent bonds with atoms or molecules. Carbon can bond in all sorts of ways that it can make long chains with other elements and molecules and they can form rings that link with other rings. This is why the atom is so diverse - it can bond with itself and other atoms so well. Carbohydrates Carbohydrates are found in grains, fruit, and vegatables. Carbohydrates provide energy to the body through glucose (a simple sugar). Carbs are represented by CH20. Types of Carbohydrates: Monosaccharides : these are simple sugars and the most common is glucose. In these 1. sugars there are usually three to six carbon atoms and they often end in -ose. They exist in a chain or ring form (ring form when aqueous). Glucose is an important sugar that gives energy for cellular respiration, photosynthesis, and other processes. Galactose and Fructose are other common monosaccharides. 2. Disaccharides : this happens when two monosaccharides go through a dehydration reaction (when one removes a water molecule) and there is a covalent bond formed in two sugar molecules. Common disaccharides are lactose, maltose, and sucrose. 3. Polysaccharides: a long chain of monosaccharides are covalently bonded. The chain could have branches or no branches and can form very large molecules. Common polysaccharides are starch, glycogen, and chitin. 1 Sunday, August 28, 2016 Starch is a form of sugar that is formed when plants synthesize glucose and create starch to store in the roots and seeds. It is also consumed by animals which they break down into smaller molecules that the cells can absorb. Glycogen is the stored form of glucose in humans that is made up of monomers of glucose which is stored in the liver and muscle cells. Cellulose is made of glucose monomers that are linked with carbon molecules that are very abundant in nature. They make up most cell walls and serve as support for the cell. Wood and paper are made of mostly cellulose. Cellulose is in a tightly packed long chain that makes it stable for the plant cells. When cellulose is in our digestive system it is called dietary fiber but the glucose bonds can not be broken down in the human body but in some animals such as cows and herbivores they can so they can use the cellulose as a food source. Arthropods such as insects, spiders, and crabs that have an exoskeleton that is made up of chitin which is repeating units of a modified sugar that contains nitrogen. Lipids Lipid are hydrophobic and will not dissolve in water due to the non polar bonds that are carbon- carbon or carbon-hydrogen. Lipids store energy for long time use in the form of a lipid called a fat and it helps keep animals and plants warm as insulation. They’re also the building blocks of a lot of hormones. Types of lipids are fats, oils, waxes, phospolipids, and steroids. Fat : are made up of glycerol and fatty acids. Glycerol is made with three carbon atoms, five hydrogen atoms, and three hydroxyl groups. Fatty acids have long chains of hydrocarbons which is attached to an acidic carboxyl in which there could be four to thirty-six carbons attached. In a fat molecule, the fatty acid is attached to three oxygen with covalent bonds. When these covalent bonds are formed, three water molecules are released and fatty acids are released that are called triglycerides because they're made of three fatty acids. Fatty acids can be saturated or unsaturated. If there are only single bonds between the carbons in the hydrocarbon chain then it is saturated. This means that the fatty acids are saturated with hydrogen and the number of hydrogen atoms attached to the carbon skeleton is maximized. If the hydrocarbon contains a double bond then the fatty acid is unsaturated. Most unsaturated fatty acids are liquids at room temperature and called oils. If there is only one double bond in an unsaturated fatty acid, it is called a monounsaturated fat and if there is more than one double bond, it is called a polyunsaturated fat. In the food industry they hydrogenate oils to increase their shelf life and they don't spoil easily and are commonly called “trans-fats. Examples of this are margarine and types of peanut butter. These types of fats can cause bad cholesterol and heart disease. 2 Sunday, August 28, 2016 Essential fatty acids are needed in your diet - like omega-3 fatty acids and they are called this because the third carbon from the end of the fatty acid has a double bond. Salmon, trout, and tuna are good sources of this and can prevent heart disease. Phospholipids: These make up the plasma membrane and are composed of two fatty-acids and a third carbon of glycerol. There are phospholipids that are hydrophobic and hydrophilic. This also makes up cell membranes Steroids and Waxes Steroids have a ring structure and are hydrophobic and all have four linked carbon rings with short tails. Cholesterol is a steroid as well as testosterone. Cholesterol makes up the plasma membranes in animal cells. Waxes are made up of hydrocarbon chains with an alcohol and fatty acid. Examples are beeswax. Plants have natural waxes like the waxy coating on leaves that helps them from drying out. Proteins Proteins are one of the most abundant molecules and has the most diverse range of functions. Each cell in the living system is made up of many types of proteins with different functions but they are all linear. Proteins can • be structural • regulatory • contractile • protect • transport • store be a part of membranes • • may be toxins or enzymes There are 20 different chemically different amino acids that form chains in many different order. Proteins can function as enzymes which are produced by living cells and are catalysts for biochemical reactions. Each enzyme is specific for the reaction to which it does and can break molecular bonds, rearrange bonds, and form new bonds. Hormones are signaling molecules that are secreted by an endocrine gland that have specific processed like growth, development, metabolism, and reproduction. Proteins have different shapes and molecular weight. The shape of a protein is conditional on tempurature, pH, exposure to other chemicals that could change shape that could lead to denaturation. 3 Sunday, August 28, 2016 Amino acids are the monomers that make up proteins. Each amino acid has the same structure: a carbon atom bonded to an amino group and a carboxyl group and a hydrogen atom. Each amino acid has another variable atom bonded to the central carbon atom which we know as R and this is the only difference between all amino acids. The chemical nature of R depends on the nature of the amino acid - whether it is acidic or basic or polar or nonpolar. The sequence of the amino acids determine the shape, size, and function of the protein. Each amino acid is attached to another amino acid with a covalent bond known as a peptide bond which is formed through a dehydration reaction. The products of the peptide bond are called polypeptides and it is technically a polymer of amino acids whereas the term protein is used for polypeptides that have combined together and have a distinct shape and function. Structure of Proteins There are four levels of protein structure 1. primary 2. secondary 3. tertiary 4. quaternary The unique and number of amino acids in the structure is the primary structure. the sequence in the protein is determined by the gene in the protein that can lead to different amino acids being added to the polypeptide chain and causing a change in the structure and function of the protein. Folding patterns can result when there are interactions between the non-R portions of the amino acids and there are secondary structures to the protein. There are common alpha helix and beta-pleated sheet structures that are held in shape by hydrogen bonds. In alpha helixes there are bonds formed between every fourth amino acids witch gives the amino acid a twisted shape. In a beta-pleated sheet, the pleats are formed when hydrogen bonds occur between the backbone of the polypeptide chains. The pleated sections extend above and below the fold and form pairs of bonds. The three-dimensional structure of the polypeptide if known as the tertiary structure which is cased by chemical reactions between various amino acids and parts of the polypeptide. Usually there are interactions of ionic or hydrogen bonding with the R groups that create a complex three-dimensional structure. In nature some proteins are made up of several polypeptides known as subunits which form the quartanary strctures. There are weak interactions that cause the stabilization of the whole structure of the protein. 4 Sunday, August 28, 2016 Nucleic Acids Nucleic acids carry the genetic blueprint of the cell and have the instructions for cell functions. There are two types of nucleic acids : deoxyribonucleic acids (DNA) and ribonucleic acids (RNA). DNA is the genetic material found in all living things and never leave the nucleus and use the RNA to communicate with the rest of the cell. RNA is involved with protein synthesis. DNA and RNA are made up of monomers called nucleotides that combine with each other to form a polynucleotide. Each nucleotide is made up of three components: a nitrogenous base, a five carbon sugar, and a phosphate group. DNA Double Helix Structure DNA has a double-helix structure which means its made up of two strands or polymers of nucleotides that are formed with bonds between the phosphate and sugar groups of nucleotides next to each other. At the bases they are bonded with hydrogen bonds and they coil around each other along the length to be a double helix (double spiral). The alternating phosphate and sugar groups lie on the outside of the strands to form the backbone of the DNA with the nitrogenous bases on the inside of the curl. 5


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