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Notes for Syllabus day and the First week of class

by: Amanda Howard

Notes for Syllabus day and the First week of class BSC1010

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These notes cover chapters 1, 2, and part of 3. Topics include: Biology and the tree of life, water and carbon, and protein structure and function.
General Biology I
Dr. Michael R. Lentz
Class Notes
Biology, phylogenetic tree, carbon, water and life, Proteins, Energy, taxonomy, Chemical Reactions, Subatomic Particles




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This 23 page Class Notes was uploaded by Amanda Howard on Saturday May 21, 2016. The Class Notes belongs to BSC1010 at University of North Florida taught by Dr. Michael R. Lentz in Summer 2016. Since its upload, it has received 78 views. For similar materials see General Biology I in Biology at University of North Florida.


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Date Created: 05/21/16
Chapter 1: Biology and the Tree of Life Key Concepts:  Organisms obtain and use energy, are made up of cells, process information, replicate, and evolve as a population  The cell theory proposes that all organisms are made of cells and that all cells come from preexisting cells  The theory of evolution by natural selection maintains that species change through time because individuals with certain heritable traits produce more offspring than other individuals do  A phylogenic tree is a graphical representation of the evolutionary relationships between species. These relationships can be estimated by analyzing similarities and differences in traits. Species that share distinctive traits are closely related and are placed close to each other on the tree of life  Biologists ask questions, generate hypotheses to answer them, and design experiments that test the predictions made by competing hypotheses What does it mean that something is alive?  All living organisms share five fundamental characteristics: o Energy : All organisms acquire and use energy  Obtained in 1 of 2 ways:  Sun energy (photosynthesis)  Eating o Cells: All organisms are made up of membrane-bound cells o Information: All organisms process hereditary information encoded in genes as well as information from the environment o Replication: All organisms are capable of reproduction o Evolution: Populations of organisms are continually evolving Theories  A theory is an explanation for a very general class of phenomena or observations that are supported by a wide body of evidence  Theories have two components: o Pattern: Something that occurs in the natural world o Process: Responsible for creating the pattern  Two theories form the framework for modern biological science: o The cell theory: What are organisms made of?  The cell is the fundamental structural unit in all living organisms o The theory of evolution by natural selection: Where do organisms come from?  All species are related by common ancestry and have changed over time in response to natural selection o These are two central unifying ideas of biology The Cell Theory  In the late 1660s, Robert Hooke and Anton van Leeuwenhoek were the first to observe cells  A cell is a highly organized compartment bounded by a plasma membrane containing concentrated chemicals in an aqueous solution o The membrane allows cells to maintain a desired set of chemicals  The cell theory states that: o All organisms are made of cells (pattern) o All cells come from preexisting cells (process)  During the time spontaneous regeneration was big (ex: flies from rotten meat) leading to Louis Pasteur’s Experiment o Working with bacteria o Boiling a broth substance to kill bacteria o Upon cooling, things grow in the broth o If you do the same heating part and seal it, nothing will grow. Things only grow if the flask is open. o Because the air cells were trapped in the swan neck and nothing grew in the flask, spontaneous generation theory was disproved.  A hypothesis is a testable statement that explains something observed o A prediction is measurable or observable result that must be correct if a hypothesis is valid o Louis Pasteur’s hypothesis:  Cells arise from cells  Cells do not arise by spontaneous generation  Van Leeuwenhoek’s Microscope Made Cells Visible. o Lens: round glass that bends light in a way that makes objects appear larger o Fluorescence microscopes o Confocal microscopy o Transmission electron microscopy  Implications of cell theory o Because all cells come from preexisting cells all individuals in a population of single-celled organisms are related by common ancestry o All of the cells present in a multicellular organisms have descended from preexisting cells and are connected by common ancestry Theory of Natural selection  In 1858, Charles Darwin and Alfred Russel Wallace made two claims regarding the natural world: o All species are related by common ancestry (pattern) o Characteristics of species can be modified from generation to generation: Descent with modification (process)  You cannot evolve; this is a population-level thing that occurs over time o Evolution: change in a population that occurs over time o Natural selection explains how evolution occurs  A population is a group of individuals of the same species living in the same area at the same time (doesn’t really work with humans because we don’t have restrictions on location)  Two conditions must be met for natural selection to occur in a population: o Individuals must vary in characteristics that are heritable o In a particular environment, certain versions of these heritable traits help individuals reproduce more than do other versions  If certain heritable traits lead to increased success in producing offspring these traits become more common in the population over time o In this way, the population’s characteristics change as a result of natural selection acting on individuals o Natural selection acts on individuals o Evolutionary change occurs in populations o Population changes due to stress provided by an environment (certain species have traits that make them more likely to survive)  Artificial selection: WE select who’s fittest to survive; we take the role of the environment o helps us understand natural selection o Changes in populations occur when humans select which individuals will produce the most offspring o Repeating this process over generations results in changes in the characteristics of a domesticated population over time o Corn ex:  Farmers wanted corn that had more protein  Take the kernels that have more protein and plant those  Artificially selected corn with a higher protein content. Differential and Reproductive success  Evolution occurs when heritable variation leads to differential success in reproduction  This variation can occur through: o Artificial selection: humans select desirable traits within a domestic population o Natural selection: traits beneficial to the current environment are “selected” within a natural population  Differences in reproductive success due to different traits Fitness and Adaptation Drive Natural Selection  Fitness is the ability of an individual to produce offspring o Individuals with high fitness produce many more surviving offspring than do others in the population  Adaptation is a trait that increases the fitness of an individual in a particular environment The Tree of Life  The cell theory and the theory of evolution by natural selection imply that all species come from preexisting species and that all species, past and present, trace their ancestry back to a single common ancestor  Speciation is a divergence process in which natural selection has caused populations of one species to diverge to form new species  The tree of life is a family tree of organisms that describes the genealogical relationships among species with a single ancestral species at its base  Phylogeny is the actual genealogical relationships among all organisms o Historically it involves what you can observe about organisms when you compare them  Using molecules to understand the tree of life o Carl Woese studied small subunit ribosomal RNA (rRNA) a molecule found in all organisms to understand evolutionary relationships o rRNA is comprised of four chemical units called ribonucleotides symbolized by letters A, U, C, and G o All cells have ribosomes. Therefore, all cells have ribosomal DNA. SO, maybe it doesn’t have to be exactly the same in every organism  Reveals relationships between species o According to the theory of evolution the sequence of ribonucleotides in rRNA can change in populations over time o Therefore, rRNA sequences should be very similar in closely related organisms and less similar in less closely related organisms  A phylogenetic tree is used to show the relationships between species o Branches that share a recent common ancestor represent species that are closely related o Branches that do not share recent common ancestors represent species that are more distantly related EX:  All organisms fall into 1 of 3 domains: o Bacteria o Archaea o Eukarya  Interpreting the tree of life o The tree of life indicates three major groups of organisms the eukaryotes: Eukarya and two groups of prokaryotes: Bacteria and Archaea  Eukaryotes – has a nucleus  Prokaryotes – no nucleus o The Tree of life shows fungi and animals are more closely related to each other than either is to plants o Traditional classification schemes were often inaccurate o The location of certain branches on the tree is hotly debated, and the shape of the tree will continue to change as databases expand Taxonomy  Taxonomy is the effort to name and classify organisms o A taxon is a named group  Domain o Woese created this new taxonomic level o It consists of three taxa:  Bacteria  Archaea  Eukarya  A phylum is a major lineage within a domain  In 1735 Carolus Linnaeus established the classification system still in use today o Each organism is given a unique two-part scientific name it consists of the genus and the species o A genus is made up of a closely related group of species o A species is made up of individuals that regularly breed together or individuals whose characteristics are distinct from those of other species  An organism’s genus and species designation is called its scientific name or Latin name o Scientific names are always italicized o Genus names are always capitalized o Species names are not capitalized o For example, Homo sapiens The nature of biology  All scientists ask questions that can be answered by measuring things—by collecting data  Science is about formulating hypotheses and finding evidence that supports or conflicts with those hypotheses o For example, using carefully designed experiments, biologists test ideas about the way the natural world works by testing the predictions made by alternative hypotheses  Hypothesis testing o Hypothesis testing is a two-step process:  State the hypothesis as precisely as possible and list the predictions it makes  Design an observational or experimental study that is capable of testing those predictions Reasons for evolution  The food competition hypothesis argues that long necks evolved because those with long necks can reach food unavailable to other mammals o Predictions:  Neck length is variable among giraffes  Neck length in giraffes is heritable  Giraffes feed high in trees o Simmons and Scheepers tested the food competition hypothesis and found o The third prediction does not hold true thus, there may be better alternative hypotheses to explain neck length in giraffes  The sexual competition theory: an alternative hypothesis is that giraffes evolved long necks because longer-necked males win more fights than shorter-necked males o Longer-necked males can then father more offspring o Data support this hypothesis o Data refute the food competition hypothesis o Another example of a sexual selection experiment: Experimental Design (Case Study: How do ants navigate)  Experiments are a powerful scientific tool because they allow researchers to test the effect of a single, well-defined factor on a particular phenomenon  Wittlinger and colleagues questioned how ants find their way back to their nest after foraging for food o Saharan desert ants meander long distances to find food (insect carcasses) but return to the nest in a straight line.  The pedometer hypothesis states that ants always know how far they are from the nest because they track the number of steps taken and they know length of their stride o Wittlinger’s group manipulated the ants into three groups after walking from the nest to a feeder (manipulated stride length):  Stumps-Legs were cut to form shorter-than-normal legs  Normal-Individuals were left alone with normal leg length  Stilts-Bristles glued on legs to form longer-than-normal legs o Then the team measured the distance the ants traveled back to the nest via a different route o Results: Results and Conclusion (con’t ant example)  A null hypothesis specifies what we should observe if the hypothesis being tested does not hold stride number and length have nothing to do with navigation (the ants use some other mechanism to navigate)-Hypothesis is incorrect  Results o “Stumps” stopped short of the nest o “Normal” ants returned to the nest o “Stilts” walked beyond the nest  Conclusion o Desert ants use information on stride length and number to calculate how far they are from the nest o Supports the pedometer hypothesis Elements of a well-designed experiment  The experiment just described is well-designed if: o included a control group (the “normal” ants) to check for other factors that might influence the outcome o Experimental conditions were controlled to eliminate other variables o The test was repeated to reduce the effects of distortion due to small sample size (Did experiment MULTIPLE TIMES and achieved the same results)  Principles of Experimental Deign o Biologists practice evidence-based decision making o Ask questions about how organisms work o Pose hypotheses to answer those questions o Use experimental or observational evidence to decide which hypotheses are correct Chapter 2: Key Water and Carbon-The Chemical basis of Life Key concepts  Molecules form when atoms bond to each other. Chemicals bonds are based on electron sharing. The degree of electron sharing varies from nonpolar covalent bonds to ionic bonds  Water is essential for life. Water is highly polar and readily forms hydrogen bonds. Hydrogen bonding makes water an extremely effective solvent  Energy is the capacity to do work or supply heat and can be (1) a stored potential or (2) an active motion. Chemical energy is a form of potential energy, stored in chemical bonds  Chemical reactions tend to be spontaneous if they lower potential energy and increase entropy (disorder). An input of energy is required for nonspontaneous reactions to occur  Most of the important compounds in organisms contain carbon. Key carbon- containing molecules formed early in earth’s history Basic Atomic Structure  Atoms are composed of three basic units: o Protons—positively charged particles o Neutrons—neutral particles o Electrons—negatively charged particles  Protons and neutrons are located in the nucleus  Electrons are found in orbitals surrounding the nucleus  As seen in the diagram above, most of the atom is empty space. The volume of the atom is comprised mostly of the electron cloud while the nucleus is usually small and dense Elements-the building blocks of chemical evolution  The atomic number: the number of protons in the nucleus o Every different atom has a characteristic number of protons in the nucleus o Atoms with the same atomic number have the same chemical properties and belong to the same element  Isotopes :forms of an element with different numbers of neutrons  Mass number :the sum of protons  neutrons of the most common isotope; the mass of the element o protons and neutrons both have a mass of 1 while the mass of electrons is negligible meaning that they do not affect the mass Electron Arrangement around the Nucleus  Electrons move around atomic nuclei in specific regions called orbitals o Each orbital can hold up to two electrons o Orbitals are grouped into levels called electron shells  Electron shells are numbered 1, 2, 3, and so on o Numbers indicate their relative distance from the nucleus o Smaller numbers are closer to the nucleus o Each electron shell contains a specific number of orbitals  An electron shell comprising a single orbital can hold up to two electrons  A shell with four orbitals can contain up to eight electrons o The electrons of an atom fill the innermost shells first, then fill the outer shells Chemical Bonding  Unfilled electron orbitals allow formation of chemical bonds  Atoms are most stable when each electron orbital is filled, so they form bonds with other atoms in order to fill their outer shell either by giving, receiving, or sharing electrons  Covalent bond-each atom’s unpaired valence electrons are shared by both nuclei to fill their orbitals o Molecules-Are substances held together by covalent bonds o electrons are shared but not always evenly, this is determined by the electronegativity of the atoms involved o Polar covalent bond occurs when the electrons are shared unevenly  the atom with higher electronegativity holds electrons more – tightly and has a partial negative charge ( ), while the other atom will have a partial positive charge ( ) o nonpolar covalent bonds occur when the electrons are shared evenly between the two atoms, therefore, the bond is symmetrical  Ionic bond occurs when electrons are transferred from one atom to another, not shared o Ion: An atom or molecule that carries a charge o Cation: An atom that loses an electron and becomes positively charged o Anion: An atom that gains an electron and becomes negatively charged o Ionic bond: The resulting attraction between oppositely charged ions  For example: in table salt(NaCl) Na gives two electron to the Cl atom creating a negatively charged Cl and a positively charged Na who attract each other  Electron sharing continuum: refers to the degree which electrons are shared in a chemical bond with the greatest sharing found in nonpolar covalent bonds, the least sharing found in ionic bonds, and the middle ground being polar covalent  How many bonds can an atom have: o The number of unpaired electrons determines the number of bonds an atom can make o Atoms with more than one unpaired electron can form multiple single bonds, double bonds, or triple bonds Representing Molecules  The shape of a simple molecule is governed by the geometry of its bonds  Molecular formulas -Indicate the numbers and types of atoms in a molecule o Example: H O2 CH 4  Structural formulas indicate which atoms are bonded together and whether the bonds are single, double, or triple bonds  Ball-and-stick models and space-filling models show molecule 3-D geometry Chemical Reactions  Chemical reactions occur when one substance is combined with another(atoms are rearranged in molecules or small molecules combine to form larger molecules) or one substance is broken down into another substance(molecules are split into atoms or smaller molecules)  In most chemical reactions, however, chemical bonds are broken and new bonds form- this event is called a coupled reaction Water  Life is based on water because water is a great solvent  The covalent bonds in water are polar, because oxygen has a greater electronegativity than hydrogen – o Oxygen has a partial negative charge ( )  o Hydrogen has a partial positive charge ( )  Hydrogen bonds: are the weak electrical attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule o They can also form between a water molecule and any other polar molecule  Hydrophilic atoms and molecules are ions and polar molecules that stay in solution o They stay in solution because of their interactions with water’s partial charges o Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water o This is because the polar nature of water pulls apart the component of the substance being dissolved  Hydrophobic molecules are uncharged and nonpolar compounds, they do not dissolve in water  Correlation of Water’s Structure and Properties o water is unique due to its structure: small size, bent shape, highly polar covalent bonds, overall polarity o Water also has several remarkable properties, largely due to its ability to form hydrogen bonds, including being:  Cohesive: binding between like molecules(binding to itself) which results in high surface tension(the  Adhesive: binding to unlike molecules  This results in the formation of the meniscus as water molecules adhere to the glass pulling upwards at the perimeter while cohesion causes water molecules at the surface form hydrogen bonds with nearby water molecules and resist the upward pull of adhesion.  denser as a liquid than a solid: this is because water expands as it changes from liquid to solid  as the diagram above illustrates the water molecules are packed much more densely in liquid form  able to absorb large amounts of energy generally in the form of heat  high specific heat  high heat of vaporization Acid-Base reactions and pH  Proton [hydrogen ion (H )] concentration is the basis of the pH scale  pH expresses proton concentration in a solution o The pH of pure water is 7 o Acids have a pH of less than 7 o Bases have a pH of greater than 7  In acid–base reactions a proton donor (acid) transfers a proton to a proton acceptor (base)  The pH scale is logarithmic:  o pH = −log [H ] o Greater H concentration  lower pH  more acidic  o Lower H concentration  higher pH  more basic/alkaline  Buffers are compounds that minimize changes in pH Chemical evolution theory  The leading scientific explanation for the origin of life o Pattern: In addition to small molecules, complex carbon-containing substances exist and are required for life o Process: Early in Earth’s history, simple chemical compounds combined to form more complex carbon-containing substances before the evolution of life  Chemical evolution may have begun in one of these environments: o The atmosphere  The dominant gases ejected by volcanoes today  Water vapor  Carbon dioxide (CO ) 2  Nitrogen (N 2  Molecular hydrogen (H ) 2may have been present)  And carbon monoxide (CO) (may have been present) o Deep-sea vents  Extremely hot  Gases such as CO an2 H 2  Reactive metals such as nickel and iron (may have been present)  Models of Chemical Evolution o Prebiotic soup model proposes that:  Certain molecules were synthesized from gases in the atmosphere or arrived via meteorites  Then condensed with rain and accumulated in oceans  Would result in an “organic soup” that allowed for continued construction of larger, even more complex molecules o Surface metabolism model suggests that:  Dissolved gases came in contact with minerals lining the walls of deep-sea vents  Formed more complex, organic molecules  Early Origin-of-Life Experiments o Stanley Miller wanted to answer a simple question:  Can complex organic compounds be synthesized from the simple molecules present in Earth’s early atmosphere?  Put another way, is it possible to re-create the first steps in chemical evolution by simulating early-Earth conditions in the laboratory? o The first step in chemical evolution  Formation of formaldehyde (H CO) 2nd hydrogen cyanide (HCN)  Requires energy input o Volcanic gases like CO, CO , 2nd H exi2ted, however, not the CH and 4 NH 3sed in Miller’s experiment o Synthesis of precursors using light energy: possible reaction in chemical evolution is the synthesis of formaldehyde (CH O) fro2 carbon dioxide and hydrogen: CO (g) 22 H (g) 2 CH 2(g)  H O2g) o Early atmosphere was dominated by:  CO 2 H 2, N ,2CO, and H 2  Reactions occur when these molecules are struck by sunlight  Sunlight represents a source of energy  High-energy photons can break molecules apart by knocking electrons away from valence shells  Photons are packets of light energy emitted by the Sun  Free radicals have unpaired electrons and are extremely unstable and highly reactive How do Chemical Reactions Happen  Chemical reactions have reactants and products o For example: CO 2g)  H 2(l)   H 2O (3q)  Chemical equilibrium occurs when the forward and reverse reactions proceed at the same rate o This causes the quantities of reactants and products remain constant  Endothermic reactions must absorb heat to proceed  Exothermic reactions release heat  What makes them spontaneous? o Chemical reactions are spontaneous if they proceed without any continuous external influence and no added energy is needed o Spontaneity of a reaction is determined by two factors: 1. The amount of potential energy- products have less potential energy than the reactants 2. The degree of order- products are less ordered than the reactants What is Energy?  Energy is the capacity to do work or supply heat  This capacity exists in one of two ways: 1. As a stored potential or potential energy  Stored energy  An object’s position determines its ability to store energy, for example  Electrons in an outer shell (farther from the  charged nucleus) have more potential energy than do electrons in an inner shell  Chemical energy is a form of potential energy in that energy is stored in chemical bonds 2. As an active motion or kinetic energy  energy of movement  measured as temperature  If an object has a low temperature:  Its molecules are moving slowly  We perceive this as “cold”  If an object has a high temperature:  Its molecules are moving rapidly  We perceive this as “hot”  Heat is the thermal energy transferred between objects of different temperatures  The first law of thermodynamics 1. Energy is conserved 2. It cannot be created or destroyed 3. It can be transferred or transformed  The second law of thermodynamics o Entropy always increases o Chemical reactions result in products with: less ordered energy and less usable energy  Entropy (S)- the amount of disorder in a group of molecules  Physical and chemical processes proceed in the direction that results in lower potential energy and increased disorder The importance of Carbon  Carbon is the most versatile atom on Earth because of its four valence electrons which allows it to form many covalent bonds  Carbon-containing molecules can form an almost limitless array of molecular shapes with different combinations of single and double bonds  The formation of carbon–carbon bonds was an important event in chemical evolution  The carbon atoms in an organic molecule furnish the skeleton that gives the molecule its overall shape  Functional group (R group) o Amino and carboxyl groups  Attract or drop a proton, respectively  Aminos act as a base  Carboxyls act as an acid o Carbonyl groups  Sites that link molecules into more-complex compounds  React to form larger molecules o Hydroxyl groups  Act as weak acids  Highly polar o Phosphate groups  Have two negative charges  Molecules with more than one phosphate linked together to store large amounts of chemical energy o Sulfhydryl groups  Link together via disulfide bonds  When present in proteins can form disulfide bonds that contribute to protein structure Chapter 3: Protein Structure and Function Key Concepts (not all of these were covered this week)  Most cell functions depend on proteins  Amino acids are the building blocks of proteins. Amino acids vary in structure and function because their side chains vary in composition  Proteins vary widely in structure. The structure of a protein can by analyzed at four levels that form a hierarchy- the amino acid sequence, substructures called alpha-helices or beta-pleated sheets, interactions between amino acids that dictate a protein’s overall shape, and combinations of individual proteins that make larger multiunit molecules  In cells, most proteins are enzymes that function as catalysts. Chemicals reactions occur much faster when they are catalyzed by enzymes. During enzyme catalysis, the reactants bind to an enzyme’s active site in a way that allows the reaction to proceed efficiently Amino Acids  All proteins are made from 20 amino acid building blocks  Structure o Amino acids have a central carbon atom that bonds to:  H—a hydrogen atom  NH —an amino functional group  COOH—a carboxyl functional group  A distinctive R-group (referred to as a side chain)  o In water (pH 7), the amino and carboxyl groups ionize to NH 3 and COO , respectively  This helps amino acids stay in solution and makes them more reactive  Side Chains (R groups) o The 20 amino acids differ only in the unique R-group attached to the central carbon o The properties of amino acids vary because their R-groups vary o Amino acid side chains distinguish the different amino acids and can be grouped into four general types:  Acidic  Basic  Uncharged polar  Nonpolar o If given a structural formula for an amino acid determine the amino acid type by asking three questions:  Does the side chain have a negative charge?  If so, it has lost a proton, so it must be acidic  Does the side chain have a positive charge?  If so, it has taken on a proton, so it must be basic  If side chain is uncharged, does it have an oxygen atom?  If so, the highly electronegative oxygen will result in a polar covalent bond and thus is uncharged polar  If the answers to all three questions are no  Then you are looking at a nonpolar amino acid o R-groups differ in their size, shape, reactivity, and interactions with water  Nonpolar R-groups: hydrophobic  Do not form hydrogen bonds  Coalesce in water  Lack charged or highly electronegative atoms capable of forming hydrogen bonds with water  Polar R-groups: hydrophilic  Form hydrogen bonds  Readily dissolve in water o Several amino acid side chains contain hydroxyl, amino, carboxyl, or sulfhydryl functional groups o These groups are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms Monomers and Polymers  Many mid-sized molecules such as amino acids and nucleotides are individual units called monomers  Monomers link together (polymerize) to form polymers such as proteins and nucleic acids  Macromolecules are very large polymers made up of many monomers linked together o Proteins are macromolecules consisting of amino acid monomers linked through chemical bonds  Assembling and breaking apart polymers o Polymerization requires energy and is nonspontaneous o Monomers polymerize through condensation (dehydration) reactions that release a water molecule o Hydrolysis is the reverse reaction that breaks polymers apart by adding a water molecule  In the prebiotic soup, hydrolysis is energetically favorable and thus would predominate over condensation. However, polymers clinging to a mineral surface are protected from hydrolysis, and thus polymerization of the amino acids into proteins may have occurred spontaneously.  Lysis means life- hydrolysis is breaking down of life by adding water  Peptide bond: Condensation reactions bond the carboxyl group of one amino acid to the amino group of another o Side chains don’t participate in polypeptide bonds o Peptide bonds are rigid o Polypeptide chains however overall flexible due to flexible rotation on other bond sites o Polypeptide: A chain of amino acids linked by peptide bonds  Within the polypeptide, the peptide bonds form a backbone with three key characteristics:  R-group orientation: Side chains can interact with each other or water  Directionality: Free amino group, on the left, is called the N-terminus while the free carboxyl group, on the right, is called the C-terminus  Flexibility: Single bonds on either side of the peptide bond can rotate, these bonds make the entire structure flexible  Oligopeptides (peptides): Polypeptides containing fewer than 50 amino acids  Proteins : Polypeptides containing more than 50 amino acids Proteins  Proteins are crucial to most tasks required for cells to exist o Catalysis: Enzymes speed up chemical reactions o Defense: Antibodies and complement proteins attack pathogens o Movement: Motor and contractile proteins move the cell or molecules within the cell o Signaling: Proteins convey signals between cells o Structure: Structural proteins define cell shape and comprise body structures o Transport: Transport proteins carry materials o Membrane proteins control molecular movement into and out of the cell o All senses are based on protein signals o Proteins break down food into amino acids  What do proteins look like? o The unparalleled diversity of proteins in size, shape, and other aspects of structure is important because: Function follows from structure o Proteins can serve diverse functions in cells because they are diverse in size and shape and diverse in the chemical properties of their amino acids o Since amino acids can be combined in limitless combinations and shapes the number of possible proteins is limitless, however, that doesn’t mean all the proteins created would be functional o All proteins have just four basic levels of structure: 1. Primary: Protein primary structure: its unique sequence of amino acids  The number of possible primary structures is practically limitless  20 types of amino acids available  Lengths range from two amino acid residues to tens of thousands  Determines everything else  If the sequence is correct then the secondary and tertiary structure should follow spontaneously  The amino acid R-groups affect a polypeptide’s properties and function  A single amino acid change can radically alter protein function 2. Secondary  Protein’s secondary structure is formed by hydrogen bonds o Hydrogen bonds occur between the carbonyl group of one amino acid and the amino group of another  Hydrogen bonding between sections of the same backbone o Is possible only when a polypeptide bends in a way that puts C  O and N–H groups close together, forming:  -helices  -pleated sheets  Or a combination of both o Each group is used for a hydrogen bond within the structure o Sidechains would stick out of the secondary coil or sheet  Secondary structure depends on the primary structure: o Some amino acids are more likely to be involved in -helices o Others are likely to be involved in -pleated sheets 3. Tertiary  The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone o These contacts cause the backbone to bend and fold o Bending and folding contribute to the distinctive three-dimensional shape of the polypeptide  The chains are folded into a stable 3D shape  Infinite possibilities, only one is correct  Structure with the lowest energy is the correct shape  R-group interactions include: o Hydrogen bonds  Form between hydrogen atoms and the carbonyl group in the peptide-bonded backbone  Or they form between hydrogen and negatively charged atoms in side chains o Hydrophobic interactions: these interactions within a protein increase stability of surrounding water molecules by increasing hydrogen bonding o Van der Waals interactions: Weak electrical interactions between hydrophobic side chains o Covalent disulfide bonds: bonds between sulfur- containing R-groups o Ionic bonds  form between groups that have full and opposing charges  Important part of the part of the folding process is in the tertiary level: o Most side chains are hydrophobic o This process happens in water o All the hydrophobic side chains are moved to the middle of the protein to minimize their interaction with water 4. Quaternary (didn’t cover this week) o Very hierarchical o Many proteins actually only have three structures o 


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