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Biology I

by: Sarah Mahmoud
Sarah Mahmoud

GPA 3.54

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These notes cover every Biology I topic. They are divided into chapter with illustrations included.
Biology I
Dr. Zambito
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This 134 page Bundle was uploaded by Sarah Mahmoud on Wednesday September 28, 2016. The Bundle belongs to BS 101 at University of the Sciences in Philadelphia taught by Dr. Zambito in Fall 2016. Since its upload, it has received 4 views. For similar materials see Biology I in Biology at University of the Sciences in Philadelphia.

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Date Created: 09/28/16
WATER AND LIFE I. Polar covalent bonds in water molecules result in hydrogen bonding. A. Water molecules share attractive forces called hydrogen bonding, but inside the molecule polar covalent bonds hold atoms together. B. Four emergent properties of water contribute to Earth’s suitability for life. o Cohesive behavior: Water molecule forms H-bonds with adjacent water molecules o Ability to moderate temperature o Expansion upon freezing o Versatility as a solvent o Adhesion: an attraction between different substances  If not for cohesion and adhesion, water molecules could not flow through plants and leave them o Surface Tension: Surface tension is measured as the energy required to increase the surface area of a liquid by a unit of area. The surface tension of a liquid results from an imbalance of intermolecular attractive forces, the cohesive forces between molecules.  Surfactant treated water droplets will form a thin film instead of beads, form smaller droplets when dripping, and water striders will sink. o High Specific Heat: Water has a lot of hydrogen bonds, and it takes heat/ energy to break those bonds.  The high specific heat of water minimizes large temperature fluctuations within bodies of water as well as within us. As water gives off heat, it is making new hydrogen bonds. o Ex- beacause San Diego and LA are next to the ocean, their temperature I moderated by the water. It absorbs the energy of the sun so it that it does not reach the cities. In inner California cities, like Palm Springs, it is hotter. o Expansion upon freezing: Water is unique because ice floats on liquid water. Rather than condensing, water expands when it freezes. Water is most dense at 4 degrees C.  At 0⁰C, water molecules become locked in a crystal lattice. This frozen lattice is why ice is less dense than liquid water  Ice actually has a very different structure than liquid water, in that the molecules align themselves in a regular lattice rather than more randomly as in the liquid form. The lattice arrangement allows water molecules to be more spread out than in a liquid, and, thus, ice is less dense than water.  If water didn’t have this property, fish would be frozen. ALL OF THESE PROPERTIES ARE RELATED TO HYDROGEN BONDING II. The Solvent of Life A. A solution is a liquid that is a homogenous mixture of substances. 1. A solvent is the dissolving agent of a solution 2. The solute is the substance dissolved 3. An aqueous solution is one in which the water is the solvent a. Water is called the universal solvent because more substances dissolve in water than in any other chemical. This has to do with the polarity of each water molecule. b. Salt, formed by ionic bonding, easily dissolves in water because the attraction to the water molecule is greater than the attraction to the other atoms in the network, so the water will pull atoms away from the network and the salt will dissolve. c. Sugars and proteins also dissolve in water. Compounds that can form hydrogen bonds or ionic bonds are soluble in water. d. The areas of water molecules with partial positive charge attract to negative molecules and the areas of water molecules with partial negative charge are attracted to molecules with positive charge. 4. Like Dissolves Like a. A hydrophilic, water loving, substance is one that has an affinity for water. A hydrophilic substance will dissolve a hydrophilic substance. b. A hydrophobic, water- fearing, substance is one that does not have an affinity for water. A hydrophobic substance will dissolve a hydrophobic substance.  Oil molecules are hydrophobic because they have relatively nonpolar bonds  This fatty acid molecule is nonpolar because this molecule is dominated by carbon and hydrogen as opposed to oxygen and nitrogen. III. Acidic and basic conditions affect living organisms A. Although water is fairly stable, a H+ ion can be transferred from one water molecule to another. +¿  H ¿ is hydronium.  1. H2O dissociates at the same rate as H 0 is 2ormed from H and OH . The concentration of H or OH ions - -7 in pure water is 10 B. An acid is a compound that gives off H+ ions in water. + - • HCl → H + Cl • HNO 3 • H SO 2 4 • HBr • HClO 3 • HClO 4 C. Bases: bases produce OH- ions in aqueous solutions. Bases ultimately reduce H+ concentrations. • LiOH • NaOH • KOH • RbOH D. Weak acids and bases 1. Weak acids and bases do not completely disassociate in solution, rather the reaction can proceed in the forward and reverse directions. - + • H2CO 3 ↔ HCO +3H + + • NH 3 H ↔ NH 4 E. Measuring Acids and Bases 1. The pH scale is a log-based scale that describes H + concentrations ([H ])  pH ranges from 1 to 14; 0 is neutral • Keep in mind that the scale is logarithmic, so a pH of 6 is 10x more acidic than a pH of 7. • A small change in pH corresponds to a large change in [H ] F. A buffer is an aqueous solution that has a highly stable pH. If you add acid or base to a buffered solution, its pH will not change significantly. Similarly, adding water to a buffer or allowing water to evaporate will not change the pH of a buffer. • A buffer is a substance that minimizes the changes in [H ] and [OH ].- • A buffer is a substance that accepts H+ ions when there are too many in solution and donates H+ ions to the solution when there are too few H+ in solution. • Buffers are important because they maintain a stable pH balance. MAJOR THEMES OF BIOLOGY 1. New properties emerge at increasing levels of biological life.  Molecules → organelles → cells → tissue → orga ns → organism → Population → community → ecosystem → biosphere 2. Everything interacts.  Organisms interact with other organisms and their environments.  The only way for new properties to emerge is with interactions of lower properties. 3. Life requires energy transfer and transformation in order to perform work.  Producers make the energy. Plants change the energy. We get energy from these sugars and so on.  Producers v. consumers; autotrophs v. heterotrophs 4. Structure determines function.  The two are always correlated. Ex- Michael Phelps is a good swimmer because of his structure.  Ex- the fins of a fish help it to propel itself through the water. The human heart serves its function as a muscular pump to get blood circulated throughout the entire body. 5. The cell is the basic unit of life. It is the smallest living thing. 6. The continuity of life requires DNA.  DNA = the heritable material of a cell. o Our genes are a section of DNA that codes for a protein. o Gene expression: expression of genes in DNA 7. Feedback mechanisms regulate biological systems. I. The Biosphere A. The Biosphere is the layer of the planet Earth where life exists. 1. The biosphere is unique. So far there has been no existence of life elsewhere in the universe. Life on Earth depends on the sun. Energy, provided as sunlight, is captured by plants, some bacteria and protists, in the marvelous phenomenon of photosynthesis. B. An ecosystem is a community of living organisms along with the non-living components of that particular environment, forming and interacting as a system, and coexisting in a sustainable manner. 1. The sun is considered as the primary source of energy, which flows in the ecosystems. This energy, in most of the cases, enters the ecosystem through plants that capture this energy through a process called photosynthesis. This energy then moves in the ecosystem through different animals, which feed on these plants or other animals. In this way the energy moves in an ecosystem and makes it sustainable. 2. Different Kinds of Ecosystems a. Aquatic Ecosystem- An ecosystem that exists in a body of water is known as an aquatic ecosystem. The aquatic ecosystems are mainly of two types, the freshwater ecosystems and the marine ecosystems. o Marine ecosystems are the biggest ecosystems. They cover around 71% of earth’s surface and also contain almost around 97% of the total water present on earth. High amounts of minerals and salts are generally present in the water in the marine ecosystems. o Freshwater Ecosystems cover only 0.8% of the earth’s surface and only account for 0.009% of the total water present on earth. There are three basic kinds of freshwater ecosystems and these are Lentic, Lotic, and Wetlands. o Many different species of reptiles, amphibians, and around 41% of the world’s fish species live in these ecosystems. The faster moving waters contain more dissolved oxygen than the slow moving waters and hence support greater biodiversity. b. Terrestrial Ecosystem- The ecosystem found only on landforms; Distinguishing factors include the shortage of water and the better availability of light. The main types are forest ecosystems, grassland ecosystems, and mountain ecosystems. o Forest Ecosystem- these ecosystems have an abundance of flora or plants. This means that these ecosystems have a high density of living organisms.  Tropical evergreen forest  Tropical deciduous forest  Temperate evergreen forest  Temperate deciduous forest and taiga. o Desert Ecosystems are defines as regions that receive an annual rainfall of less than 25 inches. Almost 17% of all land on Earth is occupied by desert.  Intense sunlight& low availability of water  Main vegetation is shrubs, bushes, and few grasses and trees. The stems and leaves of these plants are also developed in order to conserve as much water as possible.  Camels, reptiles, and some insects and birds are found in deserts. o Grassland Ecosystems are comprised of grasses with little shrubs and trees.  Grazing animals, insectivores and herbivores are the main types of organisms.  Savanna- Tropical grasslands which are dry seasonally and have a large number of predators and grazers.  Prairies are temperate grasslands which are devoid of large shrubs and trees. o Mountain Ecosystem is the most scattered and diverse in terms of the habitats that it provides.  Though the conditions at the very high altitudes can be very demanding allowing only the survival of the treeless alpine vegetation.  Another important feature about these ecosystems is that the animals that live here have thick fur coats for protection against cold and generally have a long hibernation period in the winters.  The slopes at lower altitudes are generally covered with coniferous forests. 4. Communities- an interacting group of various species in a common location. For example, a forest of trees and undergrowth plants, inhabited by animals and rooted in soil containing bacteria and fungi, constitutes a biological community. 5. Populations- The whole number of inhabitants occupying an area (such as a country or the world) and continually being modified by increases (births and immigrations) and losses (deaths and emigrations). 6. Organisms- all the unique individuals within a species 7. Organ- a portion of the body that carries out a specific function 8. Tissues- A group of cells that work together to perform a specialized function 9. Cells- the fundamental unit of structure and function 10.Organelles- Components of the cell that aid in its function 11. Molecules- made of two or more atoms II. Emergent Properties 1. Any unique property that "emerges" when component objects are joined together in constraining relations to "construct" a higher-level aggregate object, a novel property that unpredictably comes from a combination of two simpler constituents. Ex- the familiar taste of salt is an emergent property with respect to the sodium and chlorine of which it is composed. III. Cells 1. Prokaryotic vs. Eukaryotic Cells A. Prokaryotic Cells  No internal membranes, no nuclear membrane, E.R, Mitochondria, vacuoles or other organelles  Circular, naked DNA  Small Ribosomes  No cytoskeleton  Mainly unicellular  Small Cells B. Eukaryotic Cells  Distinct organelles  DNA wrapped with histone proteins into chromosomes  Ribosomes are larger  Cytoskeleton present  Multicellular with differentiation of cell types  Cells are larger IV. Heredity 1. Life’s processes involve the expression and transmission of genetic information. A. DNA is present in all cells.  The DNA molecule is a double helix consisting of two strands running in opposite directions (antiparallel) a. 5’ to 3’ (right side up); 3’ to 5’ (upside down)  DNA is a polymer consisting of repeating units of nucleotides.  5-Carbon sugar, phosphate, and a nitrogen base.  Four nitrogenous bases: Adenine, Thymine, Guanine, and Cytosine B. From DNA to protein  The triplet code in DNA is transcribed into a codon sequence in mRNA inside the nucleus.  The newly formed RNA, pre- RNA, is processed or modified inside the nucleus.  Then the codon sequence leaves the nucleus and is transcribed into an amino acid sequence (polypeptide) in the ribosome. V. Energy 1. Life requires the transfer and transformation of energy and matter A. Interactions are important in biological systems. Ex- Different interactions between carbon molecules can produce diamond or graphite. B. Organisms interact with other organisms and the physical environment. Ex- Light energy>leaves>tree>animal C. Every organism interacts with its environment, living and nonliving factors. 2. Interactions within organisms A. Positive and negative feedback i. Negative Feedback- Almost all homeostatic control mechanisms are negative feedback mechanisms. These mechanisms change the variable back to its original state or “ideal value”. a. Ex- thermostat, when blood sugar rises, the control center (pancreas) secretes insulin into the blood effectively lowering blood sugar levels. Once blood sugar levels reach homeostasis, the pancreas stops releasing insulin. ii. Positive feedback- with negative feedback, the output reduces the original effect of the stimulus. In a positive feedback system, the output enhances the original stimulus. a. Ex- child birth; during labor oxytocin is released and speeds up contractions. The increase in contractions causes more oxytocin to be released and the cycle goes on until the baby is born. The birth ends the release of oxytocin and ends the positive feedback mechanism. b. Blood clotting. Once a vessel is damaged, platelets start to cling to the injured site and release chemicals that attract more platelets. The platelets continue to pile up and release chemicals until a clot is formed. VII. Evolution: the Core Theme of Biology 1. Evolution is the idea that 2 separate organisms today have descended from a common ancestor; the theory that species change over time. It occurs through natural selection. Organisms that have certain inherited traits are better able to survive in specific environments that lack those traits. 2. Evolution accounts for the diversity and unity of life. Ex- Cilia of paramecium and cilia of windpipe cells are the same. 3. Three major domains of life:  Bacteria- prokaryotes, widespread  Achaea- prokaryotes, live in extreme environments  Eukarya- Eukaryotes  Plants  Animals  Fungi  Protists THE SCIENTIFIC METHOD  Observations- When observations can be consistently repeated, they become laws o Two different types of data: qualitative (descriptive), quantitative (numerical values) Ex- Cars develop rust faster in coastal areas  Hypothesis – Based on observations; you can never “prove” a hypothesis true. You can only support or falsify it. o Must be falsifiable and testable. Ex- Atmospheric Conditions in the coastal area hasten rusting. The chemical benzene causes cancer.  Experiment: Ex- Measure the time in which rust develops on iron nails under various conditions, such as presence of water, presence of salt and water, presence of salt alone etc. o Control (placebo) group vs. experimental group o Variables- Things you test and measure in an experiment a. Dependent: the variable being measured, will change due to independent variable. b. Independent: variable you are testing  Repeatability- In order for experiment to be reliable and valid, it must be repeated. Applies to single or Applies to all small number of events events Describes what Observation Law happens Explains why things Hypothesis Theory happen THE CHEMICAL CONTEXT OF LIFE I. Matter is anything that has mass and occupies space A. Matter is made up of elements. An element is a substance that cannot be broken down. 1. A compound is a substance consisting of two or more elements in a fixed ratio. 2. Elements of Life (in order of importance)  Hydrogen  Oxygen  Carbon  Nitrogen  Phosphorous*  Sulfur* 3. An element’s properties depend on the structure of its atoms. a. The three major subatomic particles are:  Protons (+)  Neutrons (0)  Electrons (-) b. The atomic number, the number of protons/ electrons, is what makes each element unique. Elements in the same column have similar chemical properties. c. The mass number is the number of protons+ neutrons (an approximation of the mass) Ex- 12 6 d. Valence Electrons are those in the outermost shell, or valence shell. The chemical behavior of an atom is mostly determined by valence electrons. 4. Some elements are isotopes, which have the same number of protons but differ in the number of neutrons. a. Stable Isotopes: do not decay; do not give off energy b. Radioactive Isotopes: Decay; give off energy  If a radioactive isotope decays and the number of protons changes, the element itself changes.  Radioactive isotopes can detect or cure disease. II. Chemical Bonds: The formation and function of molecules depends on chemical bonding between atoms. 1. Atoms with unfilled valence shells can share or transfer valence electrons with other atoms. These interactions result in chemical bonds. A. Main types of chemical bonds:  An ionic bond is when one atom is much more electronegative compared to the other atom. In these cases the more electronegative atom will “steal” an electron from the other atom. After the transfer, both atoms have charges and they become cations and anions. Compounds formed by ionic bonds are called salts, and are usually found in nature as crystals.  A covalent bond is formed when atoms share valence electrons. Nonpolar covalent bonds form when the electronegativity values are very similar and electrons are shared equally (ex- H , N ,methane∨CH ¿ . Polar covalent 2 2 4 bonds form when the electronegativity values are a little further apart and electrons are unequally shared. (Ex- Water) o Single covalent bond; H 2 o Double covalent bond; O 2 o Triple covalent bond;  When two metallic atoms share electrons a metallic bond may be formed. B. Electronegativity is how strong a given atom pulls the electron toward itself in a covalent bond. 2. Weak Bonds A. Hydrogen Bonds: When hydrogen atoms bind to a more electronegative atom (like O or N) a partial positive charge forms. Hydrogen bonds are between two different molecules. A hydrogen bond cannot be found within one molecule (it is not an intermolecular force) B. Van Der Waals Interactions: Even in non-polar covalent bonding, electrons can be unequally distributed. This asymmetry leads to small areas of positive and negative charges. Transient temporary distributions lead to a moment of polarity. Ex- gecko’s ability to crawl up a wall. 3. Molecular Shape and Function A. A molecule’s shape is very important to its function, which is determined by the position of its atoms’ valence orbitals. [EMERGENT PROPERTIES!] B. When someone works out, the body releases endorphins, which give a feeling of relief. Morphine, which has the same structure as endorphins, produce the same effects by mimicking endorphins and will bind to the same receptors. III. Chemical reactions make and break chemical bonds. A. Chemical reactions are often reversible. More reactants= rxn proceeds forward to produce products. More products= rxn proceeds backwards to make more reactants. CARBON AND MOLECULAR DIVERSITY I. Organic chemistry is the study of compounds that contain carbon A. Carbon can form diverse molecules by bonding to four other atoms. 1. Valence electrons determine the reactivity of an atom. Because of carbon’s valence electrons, it can bond with several other atoms. 2. Carbon can form four bonds with other atoms 3. Carbon and hydrogen for single bonds. 4. Given a chemical formula for an organic molecule, one can deduce its molecular weight and solubility in water. For example, the polar covalent bonds in sugar represent its solubility. B. Carbon skeletons can differ in the size of chains and structure. 1. Ex- Meth- (1C), eth- (2C), prop- (3C), but- (4C), pent- (5C), hex- (6C), hept- (7C), oct (8C), non- (9C), dec- (10C). Butane Iso-butane 1- Butene 2-Butene C. Hydrocarbons 1. Hydrocarbons are organic compounds consisting strictly carbon and hydrogen. 2. Lipids are composed of hydrocarbons. 3. Hydrocarbons release a LARGE amount of energy. D. Carbon bonding with atoms other than C and H 1. Carbon can also form molecules with oxygen, nitrogen, and hydrogen. (Ex- acetic acid, carbon dioxide) E. Isomers 1. Isomers are compounds with the same molecular formula but different structures and therefore different properties. Three types of isomers include structural isomers, cis-trans isomers, and enantiomers.  Structural isomers have different covalent arrangements of their atoms.  Cis- trans isomers have the same covalent bonds but differ in spatial arrangements. These molecules have different functional groups.  o Two x-s on same sides | Two x’s on opposite sides o The configuration of the double bond in an unsaturated fatty acid can take two forms ( o isomers): the naturally predominant cis form, in which both of the hydrogen atoms are on the same side of the chain; and the uncommon-in- nature trans isomer, in which the hydrogen atoms are on opposite sides. The trans form is (in most cases) best thought of as 'damaged'.  Enantiomers are isomers that are mirror images of each other.   Two enantiomers of a drug may have a different effect. There is usually only one isomer that is biologically active. This demonstrates how subtle changes can create variation in molecules and change the effect.  STRUCTURE AND FUNCTION II. A few chemical groups are key to the functioning of biological molecules A. Carbon can bind to several other atoms to make compounds with distinct properties. B. Functional groups are characteristic groups that can replace H atoms attached to C skeletons  Hydroxyl: -OH  Carbonyl: -C=O  Sulfhydryl: -SH  Amine: -NHH (Ex- Amino acids) o Can act as a base since it can accept hydrogen ions  Phosphate: -PO4 (Ex- glycerol phosphate)  Methyl: CH3 (Ex- 5 methyl- cytidine, testosterone)  Carboxyl: -COOH  Ketone  Ester  Aldehyde o The structure and function of functional groups give a molecule its properties. C. ATP: an important source of energy for cellular processes 1. One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell 2. ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups LARGE BIOLOGICAL MOLECULES I. Macromolecules A. Macromolecules are monomers built from polymers. A polymer is a long molecule consisting of many similar or identical monomers linked by covalent bonds. The four classes of biological molecules are carbohydrates, lipids, proteins, and nucleic acids. 1. The chemical mechanisms by which cells break down different polymers are the same. These processes are facilitated by enzymes, specialized macromolecules that speed up chemical reactions. Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule. This is called dehydration synthesis. In a hydrolysis reaction, polymers are disassembled to monomers by the addition of a water molecule. An example of hydrolysis is in digestion; in the digestive tract, various enzymes attack polymers, and break them down to monomer B. Carbohydrates 1. Carbs include both sugars and polymers of sugars. The simplest sugar is called a monosaccharide. a. Monosaccharides have the general molecular formula C (H O) n 2 n b. Ex- Glucose (C H6O12 6)bose (C H O5)10 5 c. Glucose and galactose are geometric isomers (they have the same chemical formula but different structure). 2. A molecule composed of two monoasaccharides is a disaccharide. A molecule composed of more than two monoasaccharides is called a polysaccharide. a. A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond between the hydroxyl group of one sugar and the Hydrogen of another sugar is called a glycosidic linkage. i. Ex- Sucrose (glucose+ fructose), Maltose (glucose+glucose), Lactose (glucose+ galactose) b. Polysaccharides are many monosaccharides linked by many glycosidic bonds. They have both storage and structural roles. The structure and function of a polysaccharide is determined by its sugar monomers and the position of its glycosidic linkages. i. Starch is a storage polysaccharide of plants, consisting entirely of glucose monomers. Starch is composed of amylose and amylopectin. (alpha linkage) ii. Glycogen is a storage polysaccharide in animals. Humans and other vertebrates store glycogen mainly in liver cells. iii. Structural polysaccharides include cellulose. Cellulose is a major component of the tough wall of plant cells. Cellulose is also a polymer of gluose, but the glycosisdic linkages differ. (Beta pleats) 3. Molecular structure of a Carbohydrate: Sugars have anywhere from 3-7 carbons. They generally contain carbonyl groups (C=O); when the carbonyl is in the middle, it is a ketone. When the carbonyl is on the end, it is an aldehyde. C. Lipids: A diverse group of hydrophobic molecules 1. Lipids have little to no affinity for water. Lipids are composed of monomers called fatty acids. A fatty acid is a long hydrocarbon chain (nonpolar) with a carboxyl group at the end (polar). The most biologically important lipids are fats, phospholipids, and steroids. a. Fats are constructed from two types of small molecules: glycerol and fatty acids. b. Triglycerides: In a fat, three fatty acids are joined to glycerol by an ester linkage (O-C=O), creating a triglyceride. c. Saturated Fats i. Saturated fats are hydrocarbon chains that contain no double bonded carbons. Since the fatty acids in these triglycerides contain the maximum possible amount of hydrogens, these would be called saturated fats. ii. The hydrocarbon chains in these fatty acids are, thus, fairly straight and can pack closely together, making these fats solid at room temperature. iii. Ex- butter, cheese d. Unsaturated Fats i. Because some of the carbons share double bonds, they’re not bonded to as many hydrogens as they could if they weren’t double bonded to each other. Therefore these oils are called unsaturated fats. ii. Because of the kinks in the hydrocarbon tails, unsaturated fats can’t pack as closely together, making them liquid at room temperature. iii. Ex- Olive oil, Canola oil e. Trans Fats i. Trans fats are artificially made fats in which hydrogens are added to unsaturated fats. Trans fats reduce HDL (good) and raise LDL (bad) cholesterol. They can be found in peanut butter, margarine, baked goods, and fries. Fatty acids with trans bonds are carcinogenic, or cancer-causing. ii. Trans fat is an unsaturated fatty acid molecule that contains a trans double bond between carbon atoms, which makes the molecule kinked. f. Phospholipids i. In a phospholipid, two fatty acids and a phosphate group are attached to glycerol. Two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head. ii. Phospholipids are the principal components of biological membranes. g. Steroids i. Steroids are lipids with a characteristic 4-ring structure. Steroids perform many biological functions from membrane integrity to hormone signaling. ii. Ex- cholesterol, sex hormones, birth control pills, cortisone, and anabolic steroids. D. Proteins: include a diversity of structures resulting in a wide range of functions. 1. Monomers of proteins are amino acids. Amino acids consist of a central carbon, which carries an amino group, a carboxyl group, hydrogen, and a side chain group. Amino acids are classified according to the solubility properties and ionizability, which they derive from their side-chains. a. Proteins are complex polymers made up of 20 different amino acids. Individual amino acids are linked by peptide bonds. Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus). 2. Structure a. A protein's primary structure is the actual sequence of amino acids. i. A slight change in primary structure may affect a protein’s structure and ability to function. Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin. b. The secondary structure refers to local bends, kinks and spirals along the chain (a helix and B pleated sheets) resulting from hydrogen bonds. c. Tertiary structure refers to the shape of the entire polypeptide chain determined by side chains. Interactions between R groups include: o Disulfide bridges (covalent bonds that reinforce tertiary structure) o Hydrogen bonds o Ionic bonds o Hydrophobic interactions o Van der Waals interactions d. Quaternary structure is used to describe proteins that consist of more than one polypeptide chain. e. Structure can be affected by alterations in pH, salt concentration, temperature, etc. Denaturation occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted. A denatured protein is biologically inactive. 3. Proteins have a wide range of functions a. Storage proteins serve to store amino acids i. Ex- Two well-known storage proteins in animals are casein and ovalbumin. Casein, found in mammalian milk, and ovalbumin, found in egg white, both provide a developing organism with a ready source of amino acids and organic nitrogen. b. Structural Proteins serve to support i. Alpha Keratin is a structural protein found in hair, skin, and nails. Collagen is the most common protein found in animals. It is a triple helix formed from three polypeptide chains. c. Enzymatic proteins selectively accelerate chemical reactions i. Enzymes are globular proteins. ii. They are active catalysts. Digestive enzymes help digest food. d. Contractile and motor proteins control movement i. Ex- Motor proteins, such as myosins and kinesins, can move along cytoskeletal filaments and this force- dependent mechanism is driven by the hydrolysis of ATP molecules. e. Hormonal Proteins serve to coordinate an organism’s activities. i. Ex- Insulin serves to regulate blood sugar levels f. Receptor Proteins are responsible for the response of cell to chemical stimuli. i. Ex- Cytokines ii. Receptor proteins participate in signal transduction, cellular signaling, gene regulation, cellular proliferation and differentiation, or regulation of cellular metabolic processes. g. Transport proteins are responsible for the transport of substances i. Transport proteins are often globular molecules. ii. Serum albumin is one example. It transports water- insoluble lipids in the bloodstream. Hemoglobin is another example. It carries oxygen from the lungs to the tissue. Myoglobin performs a similar function in muscle tissue, taking oxygen from the hemoglobin in the blood and storing it or carrying it around until needed by the muscle cells. h. Defensive proteins i. Defensive proteins protect against disease. ii. The antibodies produced by the body to fight diseases or prevent injury are called defensive proteins. Presence of an antigen or a foreign particle like bacteria, viruses, pollen or non-matching blood types, triggers the production of antibodies. iii. Fibrinogen and thrombin are antibodies that facilitate blood clotting, and prevent the loss of blood following an injury. 4. Proteins can have nonpolar side chains (hydrophobic), polar side chains (hydrophilic), or electrically charged side chains (hydrophilic). D. Nucleic Acids: store, transmit, and help express hereditary information. 1. The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene. Genes are made of DNA, which is a nucleic acid. DNA is a polymer made of nucleotide monomers. a. Two types of nucleic acids are DNA and RNA. DNA is transcribed to RNA in the nucleus and RNA leaves the nucleus to travel to the cytoplasm. RNA is then translated into proteins on ribosomes in the cytoplasm. b. DNA molecules have two polynucleotide strands spiraling around an imaginary axis, forming a double helix. The two backbones run in opposite 5’ -> 3’ directions from each other, an arrangement referred to as antiparallel. c. Both DNA and RNA are polymers of individual nucleotides. Each nucleotide has three components: o Five-carbon-ring sugar (deoxyribose or ribose) o Phosphate group o Nitrogen base o The portion of a nucleotide without the phosphate group is called the nucleoside.  DNA: Adenine, Guanine, Thymine, Cytosine  RNA: Adenine, Guanine, Uracil, Cytosine d. DNA and Evolution 1. The linear sequences of nucleotides in DNA molecules are passed from parents to offspring as genes. Two closely related species are more similar in DNA than are more distantly related species. Molecular biology can be used to assess evolutionary kinship by sequencing the DNA. CHAPTER 11 CELLULAR COMMUNICATION A. Scientists think that signaling mechanisms first evolved in ancient prokaryotes and single celled eukaryotes and were adopted for new uses by multicellular descendants. 1. Local Signaling: Eukaryotic cells may communicate by direct contact, one type of local signaling. Both plants and animals have cell junctions that directly connect the cytoplasms of adjacent cells. In this case, substances dissolved in the cytosol will pass freely between adjacent cells. a. In many cases of local signaling, messenger molecules are secreted by the signaling cell. Numerous cells can simultaneously receive and respond to the molecules of growth factor produced by a single cell in their vicinity. This type of local signaling in animals is called paracrine signaling. 2. Gap junctions: Both animals and plants have cell junctions that allow molecules to pass between adjacent cells without crossing the plasma membrane. 3. Cell-to-Cell recognition (aka contact dependent): Animal cells may communicate via direct contact between membrane bound cell surface molecules in a process called cell-to-cell recognition. This signaling is important to embryonic development and the immune response. [Auto- self (regulation); Para- next to(regulating cells around you)] In autocrine and paracrine regulation, the molecules have to get out then get back in. 4. Long Distance Signaling: Both animals and plants use chemicals called hormones for long- distance signaling. In hormonal signaling in animals, known as endocrine signaling, specialized cells release hormone molecules, which travel via the circulatory system to other parts of the body. Hormonal signals must travel through the bloodstream. a. Plant hormones, called plant growth regulators, sometimes travel in vessels but more often reach their targets by moving through cells or diffusing through air. b. Ex-A deaf person cant hear sound waves coming in c. Liver& kidney cells don’t have the appropriate receptors and cant respond to the signals 5. Three Stages to A Signal  Reception: Reception is the target cell’s detection of a signaling molecule coming from outside the cell. A chemical signal is “detected when the signaling molecule binds to a receptor protein located at the cell’s surface or inside the cell.  Transduction: The binding of the signaling molecule changes the receptor protein in some way, initiating transduction. Transduction converts the signal to a form that can bring about a specific cellular response. Transduction sometimes occurs in one step but most often occurs in a series of steps called a signal transduction pathway.  Response: In the third stage of cell signaling, the transduced signal finally triggers a specific cellular response.. B. Reception: A signaling molecule binds to a receptor protein, causing it to change shape 1. Receptor molecules are very specific for the signaling molecule. The signaling molecule is complementary in shape to a specific site on the receptor and attaches there, like a key in a lock, and activates the receptor. This enables it to interact with other cellular molecules. The signaling molecule is a ligand. Cells have tens of thousands of receptors embedded in the cell membrane, or in the cytoplasm and nucleus. Most signaling receptors are plasma membrane proteins, but others are located inside the cell. a. If you have a polar protein, can it pass through the membrane? No it cannot pass through the membrane. It needs a “helper”. The cell needs a receptor to recognize the signal. Ligands (signaling molecules) must bind to the receptor of the cell membrane b. Ligand binds to Cell Surface Receptor > Ion Channels open > Sometimes ligands bind to receptors that are also ion channels > When the ligand binds, the receptor changes shape and opens an ion channel. There is no transduction; the receptor itself is able to recognize the signal and is able to respond i. Acetylcholine binds to one channel and opens another to sodium. C. Ligand binds to Cell Surface Receptor –> Signal transduction, G protein 1. A G- Protein coupled receptor (GPCR) is a cell surface transmembrane receptor that works with the help of a G- protein, a protein that binds the energy rich molecule GTP. GCPR proteins are similar but differ in their binding sites.  Ligand binds to the receptor and changes the shape of the receptor.  This change in shape can activate other molecules (G- protein).  The G-protein then activates a cellular enzyme  The enzyme performs a specific job in the cell. Eventually the G protein will leave the enzyme, which returns to its original state. The G protein is now available for reuse. D. Ligand binds to Cell Surface Receptor – Signal transduction, RTK 1. Receptor Tyrosine Kinases belong to a major class of plasma membrane receptors characterized by having enzymatic activity. A kinase is any enzyme that catalyzes the transfer of phosphate groups. RTKs attach phosphates to tyrosines.  Ligand binds to a tyrosine kinase receptor (RTK) (when no ligand is bound, the receptor is inactive)  Adjacent binding causes dimerization (ie conformational change)  The dimers activate one another by cross-phosphorylation.  The phosphorylated receptors activate other cellular proteins for a response. 2. Cancer is known to arise from dysregulated RTK pathways. Normally, ligands need to bind to activate receptors. In cancer cells, the ligand is not needed. Therefore they keep dividing. For example, breast cancer patients have poor prognosis if their tumor cells harbor excessive levels of a receptor tyrosine kinase called HER2. 3. All of these examples depend on a polar molecule binding to a receptor embedded within the cell membrane. a. What if a non-polar molecule were a signaling molecule? It is able to bypass the membrane, therefore it does not need to bind to the membrane. Where could it bind? Receptors in the cytoplasm or nucleus E. Ligand binds to Intracellular Receptor 1. Intracellular receptors proteins are found in either the cytoplasm of nucleus of target cells. To each receptor, a signaling molecule passes through the target cell’s plasma membrane if they are hydrophobic or small enough. a. Some of these hydrophobic chemical messengers include steroid hormones and thyroid hormones. Nitric oxide is another. 2. Major cellular effects a. Steroid hormone signaling: Once a hormone has entered a cell, it may bind to an intracellular receptor in the cytoplasm or nucleus. This will change the receptor into a hormone receptor complex that is active and can turn particular genes on or off. b. (Ex- aldosterone) 3. Activated Transcription Factor a. Transcription factors are special proteins which control which genes are turned on, or which genes are transcribed into mRNA in a particular cell at a particular time. A non-polar ligand passes through the cell membrane, binds to an intracellular receptor and activates it. The activated receptor enters the nucleus. The activated receptor binds to the DNA and acts as a transcription factor. DNA is transcribed to RNA. RNA is then translated to protein. 4. Protein molecule: activating enzymes (through phosphorylation), open ion channels a. Which best describes what a plasma membrane spanning receptor does upon reception of a signal? Binding of the signal molecules alters the receptor’s other binding sites and activities. b. NGF(nerve growth factor) is a water soluble signaling molecule. It is expected that the receptor be in the cell membrane. CHAPTER 16: THE MOLECULAR BASIS OF INHERITANCE I. DNA is the genetic material A. T.H. Morgan showed genes exist as parts of chromosomes. Prior to the 1940’s it was not known that DNA coded for inherited materials. The case for proteins seemed stronger, since scientists saw them as a class of macromolecules with great heterogeneity& specificity of function. Nucleic acids were too uniform to provide heterogeneity. B. Today we routinely manipulate DNA in the lab to see what the manipulation changes. 1. Scientists put GFP in pigs, a gene that causes their skin to be glow in the dark. II. Figuring Out the Structure of DNA A. Initially all Watson and Crick knew was that DNA is a polymer of nucleotides composed of a nitrogenous base, a sugar, and a phosphate group. 1. Crick was studying x-ray crystallography, and Watson knew the kind of x-ray diffraction pattern that helical molecules produced. The photograph of Rosalind Franklin’s x- ray diffraction of DNA confirmed DNA was a helical shape. It also confirmed the width of the helix& spacing of nitrogenous bases. 2. The pattern also implied the helix was made of two strands, contrary to the three strand model Pauling proposed. This accounts for the term “double- helix” 3. Watson& Crick built models conforming to Chargaff’s rule of base equivalences and Franklin’s discovery that the sugar-phosphate backbones were on the outside of the DNA model, contrary to what they’d thought. a. Franklin’s arrangement was good because it put the hydrophobic nitrogenous bases in the interior, away from the surrounding aqueous solution and the negatively charged phosphate groups wouldn’t be forced together. b. In their model, the sugar phosphate backbones are antiparallel. Also, A pairs with T and C pairs with G. A&G are purines, two ringed, and C&T are pyrimidines, single ringed. B. Erwing Chargaff reported in any species the number of A and T bases are equal and the number of G and C bases are equal 1. The number of A+T and G+C varies between species. But at the time, he did not know that A and T bind, and G and C bind (see left) C. Watson and Crick and Maurice Wilkins won the Nobel Prize. III. Many proteins work together in DNA replication and repair A. The Basic Principle: Base Pairing to a Template Strand 1. “ It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” 2. Since the two strands of DNA are complementary, each strand acts as a template for building a new strand in replication. a. In DNA replication, the parent molecule unwinds, and two new daughter strands are built based on base-pairing rules. b. Where there was one double stranded DNA molecule, there are soon two, each an exact replica of the “parent” c. Analogous to using a photographic negative to make a positive to make another negative& so on. B. Models of Replication 1. Semiconservative: When a double helix replicates, each two daughter molecules will have one strand, from the parent molecule& a newly made strand 2 . Conservative: Two parental strands come back together after the process (parent molecule conserved) 3. Dispersive: All four strands of DNA following replication have a mixture of old and new DNA. 4. All three models remained until they could be ruled out. a. The results of Watson& Crick’s experiment supported the semiconservative model of DNA replication C. DNA Replication: A Closer Look 1. The copying of DNA is remarkable in its speed and accuracy. Each cell has 46 DNA molecules in the nucleus. 2. More than a dozen enzymes and other proteins participate in DNA replication a. Getting Started  Replication begins at particular sites called origins of replication (short stretches of DNA with a specific sequence), where the two DNA strands are separated, opening up a replication “bubble” o Eukaryotic chromosomes may have hundreds or thousands of replication origins  Replication proceeds in both directions from each origin, until the entire molecule is copied  At the end of each replication bubble is a replication fork, a y shaped region where the parental strands of DNA are being unwound o Helicases are enzymes that untwist the double helix at the replication fork o Topoisomerases b. Synthesis of DNA i. Enzymes called DNA polymerases catalyze the elongation of new DNA at a replication fork. They add nucleotides to a preexisting chain.  Each nucleotide to be added consists of a sugar attached to a base and three phosphate groups ii. Most DNA polymerases require a primer and a DNA template strand. The initial nucleotide chain that’s produced during DNA synthesis is actually RNA not DNA, called a primer. • DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end • An enzyme called primase can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template • The primer is short (5–10 nucleotides long), It is thus base paired to the template strand. The 3’ end serves as the starting point for the new DNA strand. 3. Antiparallel Elongation a. Each DNA strand has directionality. The two strands are antiparallel. Therefore the two new strands of DNA formed must also be antiparallel to their template strands b. Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork i. DNA polymerase can only add to the free 3’ end of a primer or growing DNA, never the 5’ and. A new strand can only elongate in the 5’ -> 3’ direction. ii. The DNA strand made by this is called the leading strand. Only 1 primer is required to synthesize the entire leading strand. c. To elongate the other new strand in the 5’->3 direction, DNA polymerase must work in the direction away from the replication fork. The DNA strand elongating in this direction is called the lagging strand. d. In contrast to the leading strand, the lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase D. Proofreading and Repairing DNA 1. DNA polymerases proofread DNA as it is being made. Newly synthesized incorrect nucleotides are removed and replaced. 2. In a mismatch repair, other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors. a. A hereditary defect in one of them is associated with a form of colon cancer; they’re important. 3. In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA. The resulting gap is filled with nucleotides, using the undamaged strand as a template. IV. Nucleotide Excision Repair A. A DNA repair system called a nucleotide excision repair involves a DNA polymerase and DNA ligase A TOUR OF THE CELL I. Microscopy A. Microscopes were invented in 1950 and refined in the 1600s. Robert Hooke first saw cell walls in 1665 as he looked at dead cells from the bark of an oak tree through a microscope. Anton van Leeuwenhoek’s better lenses helped visualize living cells, and he called them “very little animalcules”. B. The microscopes first used by Renaissance scientists are called light microscopes (LM). Visible light is passed through the specimen and then through glass lenses that bend a light in such a way that the image of the specimen is magnified as it is projected into the eye. 1. Magnification is the ratio of an object’s image to its real size. 2. Resolution is a measure of the clarity of the image, or the minimum distance two points can be separated and still be distinguished as two points. 3. Contrast accentuates the differences in parts of the sample. C. Until recently, the resolution barrier prevented cell biol


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