The science of biology

Introduction Exploring life The Science of Biology Biology is Studied Using the Scientific Method Science is based on a systematic thought process Deductive reasoning - Summarize the information at hand and draw conclusions from that information proceeds from the general to the specific Inductive reasoning - Drawing a generalization from several specific observations proceeds from the specific to the general Must be careful because it is impossible to prove the accuracy of the generalization Observations testable models and experiments The scientific method is a recursive process for discovering knowledge that involves making observations making testable models and conducting experiments First step involves collecting information and or summarizing existing observations about the phenomenon under study This permits the formulation of a hypothesis a testable model that explains the existing observations and makes predictions that can be tested An experiment is conducted to test the correctness of the hypothesis Experimental or treatment group - the individuals given the specific treatment or condition being tested Control group - the individuals not given the specific treatment Observation and measurement of the experimental and control groups and comparison of the data obtained provides evidence to either support or reject the hypothesis Care must be taken that the experimental and control groups receive the same treatments except for the specific effect being tested Example the placebo effect The recursive nature of the process experiments provide more observations and at any time more observations may be added in and more testable models may be produced this may in turn lead to more experiments and the process continues This generally leads to progress towards more and more reliable models of how nature works Creative thinking often plays a major role when rapid progress occurs Hypothesis theory and law A well supported hypothesis that links together a large body of observations is considered a theory A theory that links together significant bodies of thought and yields unvarying and uniform predictions over a long period of time becomes considered a principle or law The supernatural by definition is outside the bounds of science Supernatural causes and effects cannot be proved or disproved science and technology the goal of science is to understand nature the goal of technology is to apply scientific knowledge for a specific purpose Characteristics of Living Matter Living things are composed of cells Cell - The basic structural and functional unit of life consisting of living material bounded by a membrane The smallest unit of living things capable of growth and development Unicellular - An organism consisting of a single cell Multicellular - An organism consisting of more than one cell Living things grow and develop Growth-increase in size because number of cells or size of cells increases Development-changes in roles of cells during the life cycle of an organism Metabolism includes the chemical processes essential to growth and repair Metabolism - the sum of the chemical reactions and energy transformations that take place within a cell Homeostasis - the tendency of an organism to maintain a relatively constant internal environment Living things respond to stimuli stimulus - physical or chemical changes in the internal or external environment of an organism Living things reproduce Asexual reproduction copying reproduction not involving sex genetic recombination resulting from only cell division Sexual reproduction reproduction involving sex typically involves the formation of specialized egg and sperm cells and their fusion to produce a zygote which grows and develops into a new organism Information Transfer in Living Systems Information must be transferred from one generation to the next DNA deoxyribonucleic acid is responsible for information transfer from one generation to the next DNA is the chemical substance that makes up genes the units of heredity Information must be transferred from one cell generation to the next Information is exchanged between cells Hormones are chemical signals used for intercellular signaling Physical signals also lead to intercellular communication e g nerve cells Biological Organisms Show Great Diversity Biologists use a binomial system for classifying organisms Taxonomy - the science of classifying and naming organisms Carolus Linnaeus th century Swedish botanist developed a system of classification that is the basis of what is used today Species - basic unit of classification or taxonomy if sexual a group of organisms that can interbreed and produce fertile offspring if asexual grouped based on similarities DNA sequence is best about million living species have been described likely millions more Genus - a group of closely related species Together the genus and specific epithet names make up the binomial name used to name a species The Genus name is always capitalized and the specific epithet is never capitalized The Genus and specific epithet are always together and italicized or underlined Example Homo sapiens or Homo sapiens Taxonomic classification is hierarchical A group of related genera make up a Family Related families make up an Order Related orders are grouped into a Class Related classes are grouped into a Phylum or Division Related phyla or divisions are grouped into a Kingdom Related kingdoms are grouped into a Domain the highest level of classification in the modern system The gold standard for related is based on DNA sequence similarities but other criteria are used as well we don t have the complete DNA sequence of all known species The most widely accepted classification system today includes three domains and six kingdoms Two domains consist of prokaryotes organisms with no true cellular nucleus Domain Archaea Kingdom Archaebacteria bacteria typically found in extreme environments distinguished from other bacteria mainly by ribosomal RNA sequence include methanogens extreme halophiles and extreme thermophiles Domain Bacteria Kingdom Eubacteria very diverse group of bacteria examples blue-green algae Escherichia coli One domain Eukarya consists of eukaryotes organisms with a discrete cellular nucleus it is divided into four kingdoms Kingdom Protista Single celled and simple multicellular organisms having nuclei and not fitting into the other three eukaryotic kingdoms Includes protozoa algae water molds and slime molds Kingdom Plantae Plants are complex multicellular organisms having tissues and organs Plant cells have walls containing cellulose as the main structural component Most are photosynthetic and those that are have chlorophyll in chloroplasts Kingdom Fungi Organisms with cell walls containing chitin as the main structural component Most are multicellular Most are decomposers Includes molds and yeasts as well as mushrooms etc Kingdom Animalia Complex multicellular organisms that must eat other organisms for nourishment No cells walls Typically have organs and organ systems Most forms are motile Life Depends on a Continuous Input of Energy At the cellular level part of the energy that is obtained from nutrients is utilized to synthesize new cellular components Used for maintenance of existing cellular structures and components replacement of damaged or worn out materials within the cell Used to produce materials to support growth development and reproduction Part of the energy obtained from nutrients is used to support Movement either of cell itself or of materials into and out of the cell Signaling responses such as hormone production and perception nerve impulses etc Other forms of cell work such as symbiotic relationships with other organisms defense against pathogens Energy flows through ecosystems the concept of a food chain or food web Producers autotrophs manufacture their own food from simple materials usually produce food by the process of photosynthesis Carbon dioxide Water light energy Carbohydrate food Oxygen use such food by oxidative respiration Carbohydrate food Oxygen Carbon dioxide Water energy overall producers use carbon dioxide and water and release food and oxygen Consumers heterotrophs obtain energy by eating other organisms ultimate source of food is producers use food and oxygen and release carbon dioxide and water Decomposers obtain energy by breaking down the waste products by products and dead bodies of producers and consumers Usually bacteria and fungi Themes that pervade biology The cell Information management Energy management Structure and function Unity and diversity Emergent properties Evolution the core unifying theme Chapter Introduction The Science of Biology Discuss in your group how the scientific method works and the difference between inductive and deductive reasoning Come up with examples of inductive and deductive reasoning Do NOT worry about learning the scientific method as step one step two etc Discuss testable models including terms for them and why testable matters How does this relate to the supernatural Explain the characteristics of living matter to each other Answer the Fido question will be given in class Discuss the role of information in life and how it is dealt with on the molecular level Explain to each other the binomial system and taxonomic hierarchy What is a species name What do the two words in a species name represent and how do you write them How will you memorize the hierarchy What are the three domains and six kingdoms How do you decide which kingdom to put a eukaryote into What is the importance of energy in living systems What are autotrophs and heterotrophs Biology is Studied Using the Scientific Method Science is based on a systematic thought process Deductive reasoning - Summarize the information at hand and draw conclusions from that information proceeds from the general to the specific Inductive reasoning - Drawing a generalization from several specific observations proceeds from the specific to the general Must be careful because it is impossible to prove the accuracy of the generalization Observations testable models and experiments The scientific method is a recursive process for discovering knowledge that involves making observations making testable models and conducting experiments First step involves collecting information and or summarizing existing observations about the phenomenon under study This permits the formulation of a hypothesis a testable model that explains the existing observations and makes predictions that can be tested An experiment is conducted to test the correctness of the hypothesis Experimental or treatment group - the individuals given the specific treatment or condition being tested Control group - the individuals not given the specific treatment Observation and measurement of the experimental and control groups and comparison of the data obtained provides evidence to either support or reject the hypothesis Care must be taken that the experimental and control groups receive the same treatments except for the specific effect being tested Example the placebo effect The recursive nature of the process experiments provide more observations and at any time more observations may be added in and more testable models may be produced this may in turn lead to more experiments and the process continues This generally leads to progress towards more and more reliable models of how nature works Creative thinking often plays a major role when rapid progress occurs Hypothesis theory and law A well supported hypothesis that links together a large body of observations is considered a theory A theory that links together significant bodies of thought and yields unvarying and uniform predictions over a long period of time becomes considered a principle or law The supernatural by definition is outside the bounds of science Supernatural causes and effects cannot be proved or disproved science and technology the goal of science is to understand nature the goal of technology is to apply scientific knowledge for a specific purpose Characteristics of Living Matter Living things are composed of cells Cell - The basic structural and functional unit of life consisting of living material bounded by a membrane The smallest unit of living things capable of growth and development Unicellular - An organism consisting of a single cell Multicellular - An organism consisting of more than one cell Living things grow and develop Growth-increase in size because number of cells or size of cells increases Development-changes in roles of cells during the life cycle of an organism Metabolism includes the chemical processes essential to growth and repair Metabolism - the sum of the chemical reactions and energy transformations that take place within a cell Homeostasis - the tendency of an organism to maintain a relatively constant internal environment Living things respond to stimuli stimulus - physical or chemical changes in the internal or external environment of an organism Living things reproduce Asexual reproduction copying reproduction not involving sex genetic recombination resulting from only cell division Sexual reproduction reproduction involving sex typically involves the formation of specialized egg and sperm cells and their fusion to produce a zygote which grows and develops into a new organism Information Transfer in Living Systems Information must be transferred from one generation to the next DNA deoxyribonucleic acid is responsible for information transfer from one generation to the next DNA is the chemical substance that makes up genes the units of heredity Information must be transferred from one cell generation to the next Information is exchanged between cells Hormones are chemical signals used for intercellular signaling Physical signals also lead to intercellular communication e g nerve cells Biological Organisms Show Great Diversity Biologists use a binomial system for classifying organisms Taxonomy - the science of classifying and naming organisms Carolus Linnaeus th century Swedish botanist developed a system of classification that is the basis of what is used today Species - basic unit of classification or taxonomy if sexual a group of organisms that can interbreed and produce fertile offspring if asexual grouped based on similarities DNA sequence is best about million living species have been described likely millions more Genus - a group of closely related species Together the genus and specific epithet names make up the binomial name used to name a species The Genus name is always capitalized and the specific epithet is never capitalized The Genus and specific epithet are always together and italicized or underlined Example Homo sapiens or Homo sapiens Taxonomic classification is hierarchical A group of related genera make up a Family Related families make up an Order Related orders are grouped into a Class Related classes are grouped into a Phylum or Division Related phyla or divisions are grouped into a Kingdom Related kingdoms are grouped into a Domain the highest level of classification in the modern system The gold standard for related is based on DNA sequence similarities but other criteria are used as well we don t have the complete DNA sequence of all known species The most widely accepted classification system today includes three domains and six kingdoms Two domains consist of prokaryotes organisms with no true cellular nucleus Domain Archaea Kingdom Archaebacteria bacteria typically found in extreme environments distinguished from other bacteria mainly by ribosomal RNA sequence include methanogens extreme halophiles and extreme thermophiles Domain Bacteria Kingdom Eubacteria very diverse group of bacteria examples blue-green algae Escherichia coli One domain Eukarya consists of eukaryotes organisms with a discrete cellular nucleus it is divided into four kingdoms Kingdom Protista Single celled and simple multicellular organisms having nuclei and not fitting into the other three eukaryotic kingdoms Includes protozoa algae water molds and slime molds Kingdom Plantae Plants are complex multicellular organisms having tissues and organs Plant cells have walls containing cellulose as the main structural component Most are photosynthetic and those that are have chlorophyll in chloroplasts Kingdom Fungi Organisms with cell walls containing chitin as the main structural component Most are multicellular Most are decomposers Includes molds and yeasts as well as mushrooms etc Kingdom Animalia Complex multicellular organisms that must eat other organisms for nourishment No cells walls Typically have organs and organ systems Most forms are motile Life Depends on a Continuous Input of Energy At the cellular level part of the energy that is obtained from nutrients is utilized to synthesize new cellular components Used for maintenance of existing cellular structures and components replacement of damaged or worn out materials within the cell Used to produce materials to support growth development and reproduction Part of the energy obtained from nutrients is used to support Movement either of cell itself or of materials into and out of the cell Signaling responses such as hormone production and perception nerve impulses etc Other forms of cell work such as symbiotic relationships with other organisms defense against pathogens Energy flows through ecosystems the concept of a food chain or food web Producers autotrophs manufacture their own food from simple materials usually produce food by the process of photosynthesis Carbon dioxide Water light energy Carbohydrate food Oxygen use such food by oxidative respiration Carbohydrate food Oxygen Carbon dioxide Water energy overall producers use carbon dioxide and water and release food and oxygen Consumers heterotrophs obtain energy by eating other organisms ultimate source of food is producers use food and oxygen and release carbon dioxide and water Decomposers obtain energy by breaking down the waste products by products and dead bodies of producers and consumers Usually bacteria and fungi Themes that pervade biology The cell Information management heritable information regulation and interaction with the environment Energy management Structure and function Unity and diversity Emergent properties Evolution the core unifying theme that explains much of the observations connected with the other themes In addition an awareness of the process scientific inquiry and the application of science technology are important aspects of any study of biology Chapter The chemical context of life You must understand chemistry to understand life and to pass this course Overview In many ways life can be viewed as a complicated chemical reaction Modern models of how life works at all levels typically have at least some aspect of chemistry as a major component or underpinning Elements and Atoms elements substances that cannot be further broken down into other substances at least by ordinary chemical reactions every element has a chemical symbol H for hydrogen O for oxygen etc this is most familiar from the periodic table there are naturally occurring elements from hydrogen up to uranium elements oxygen carbon hydrogen and nitrogen O C H N make about of the mass of most living things others are consistently present in small amounts in living things Ca P K S Na Mg Cl Fe several others are typically found only in trace amounts trace elements these tend to vary considerably in amount and even presence depending on the type of organism an atom is the smallest unit of an element that still retains the properties of that element atoms consist of subatomic particles electron - contributes no significant mass to the atom but carries a - electrical charge proton - contributes a mass of approximately mass unit and carries a electrical charge neutron - contributes a mass of approximately mass unit and carries no net electrical charge protons and neutrons are found in the nucleus center of an atom elements differ from each other because they contain different numbers of protons all hydrogen atoms contain proton all carbon atoms contain protons all oxygen atoms contain protons etc atomic number number of protons in the nucleus the periodic table has elements arranged largely according to atomic number protons neutrons determine atomic mass each contribute atomic mass unit amu or Dalton atoms that have the same number of protons but have different numbers of neutrons therefore different masses are referred to as isotopes atomic nuclei can undergo changes decay some elements are more stable than others some isotopes are more stable than others most unstable radioisotopes decay rates are statistical averages and are used for measuring time passage in many areas of science carbon dating etc the radiation emitted upon decay alpha beta and or gamma can be used as a tool for experiments can also be used medically has other uses and dangers nuclear power nuclear bombs radiation poisoning etc radiation can cause mutations in DNA can interfere with cell division electrons occupy orbitals surrounding the nucleus and move at the speed of light because ATOMS are electrically neutral the number of electrons an atom has always equals the number of protons electrons can exist at different energy levels which correspond to orbitals the further away an orbital carries an electron from the nucleus the higher the energy level of the electron electrons with similar energies make up an electron shell the outer electron s are known as the valence electron s collectively they occupy the valence shell the chemical properties of an atom are largely determined by the valence electrons the science of chemistry mostly involves study of how electrons move about the nucleus store energy and determine chemical properties of substances as a result Describing Atomic Combinations atoms combine to form molecules and compounds molecule two or more atoms held together by covalent bonds defined later may be composed of one or more elements examples O H O not all substances are molecular NaCl table salt isn t if a substance is molecular then an individual molecule is the smallest unit of the substance that exhibits the properties of the substance thus a molecule differs in its physical and chemical properties from the elements that make it up compound - a specific combination of two or more different elements chemically combined in a fixed ratio compounds have unique physical and chemical properties that differ from those of the elements used to make it some compounds are held together by covalent bonds and are therefore molecular some are held together by ionic bonds defined later chemists use two types of formulas to describe substances chemical formula - a shorthand formula showing the number of atoms of each element present in a molecule often called molecular formula if a molecule is involved examples H O CO O C H O follows simplest ratio for ionic substances NaCl etc structural formula - shows the arrangement of atoms in a molecule examples water H O H carbon dioxide O C O molecular oxygen O O the number of units of a substance are described using the mole molecular mass is the sum of the atomic masses of the atoms in the molecule since the actual mass of an atom is extremely small it is convenient in the real world to work with a large number of atoms at the same time The amount of a substance that in grams has the same number as the atomic mass is a mole Thus water has molecular mass a mole of water has a mass of g The mole is simply a conversion factor from the small scale of atomic mass units to the more familiar gram scale the factor represents the number of units molecules or atoms in a mole this factor called Avogadro s number is x atoms or molecules Chemical Bonds Hold Molecules Together and Store Energy recall that electrons in the outermost shell of an atom valence electrons determine the chemical behavior of the atom i e what type and how many chemical bonds it can readily form most atoms in biological systems seek to have electrons in their outermost shell hydrogen seeks to have or electrons in its outermost shell since atoms have the same number of electrons as protons they meet this need to have a full valence shell by sharing giving up or acquiring electrons from other atoms this forms chemical bonds a chemical bond is a reduced energy state bond energy is the amount of energy required to break a particular chemical bond there are two principle types of strong chemical bonds covalent bonds - electrons are shared between two atoms ionic bonds - one atom completely gives up an electron to another atom covalent bonds result in filled valence shells electrons are shared in pairs a single electron pair shared a single covalent bond double and triple covalent bonds are also possible carbon forms covalent bonds covalent bonds give molecules definite shapes the shared atomic orbitals require definite spatial arrangements that depend on the atoms involved in the bond covalent bonds can be nonpolar equal sharing of electrons or polar unequal sharing of electrons polar bonds result if one nucleus holds a stronger attraction on the electron pair molecules with polar bonds polar molecules have regions with partial charges ionic bonds when an atom gains or gives up one or more electrons it is called an ion cations - ions that have lost one or more electrons have a positive charge anions - ions that have gained one or more electrons have a negative charge the suffix ide indicates an anion polyatomic ions can also form covalently bound atoms that lose or gain electrons or protons only polyatomic ions can lose or gain protons polyatomic cations positive charge polyatomic anions negative charge an ionic bond is formed by the attraction between a cation and an anion an ionic compound is a substance held together by ionic bonds ionic compounds dissociate into individual ions when dissolved in a polar substance such as water hydration surrounding the ions with the ends water molecules with the opposite partial charge hydrogen bonds weak interactions involving partially charged hydrogen atoms the interaction is with another atom with a partial - charge can be within the same large molecule or between molecules hydrogen bonds are common and important in living things water forms hydrogen bonds because they are weak hydrogen bonds are relatively easy to manipulate collectively hydrogen bonds can be very strong they hold together the two strands of DNA for example In aqueous systems such as living organisms the effective relative bond strengths are covalent bond ionic bond hydrogen bond Chemical Equations Describe Chemical Reactions Reactants are written on the left Products are written on the right an arrow is used to show the direction the reaction proceeds C H O O CO H O Energy double arrows of equal lengths indicate equilibrium reactions reactions proceeding simultaneously at equal rates in both directions N H NH Sometimes different lengths of double arrows are used to indicate which direction is favored CO H O H CO Oxidation-Reduction Reactions redox reactions Are Common in Biological Systems oxidation is a chemical process in which an atom molecule or ion loses an electron s reduction is the opposite an electron is gained charge is reduced oxidation and reduction are always paired hence redox reactions example rusting when iron rusts iron oxide is formed by the oxidation of iron this can be described by a chemical reaction as shown below Fe O Fe O during the process iron atoms Fe become iron ions Fe Fe Fe e- therefore we can say that iron atoms were oxidized to produce iron ions above on the flip side the oxygen atoms gain electrons we can say that the oxygen is reduced in the reaction O e- O - oxygen is the most common oxidizing agent hence the general term oxidation in biological systems typically molecules are oxidized and reduced very important in many processes such as photosynthesis respiration electrons are less easily lost from molecules than from atoms molecules typically will lose the equivalent of a complete hydrogen atom when oxidized this means that both a proton and an electron are removed from the oxidized molecule and may be added to the reduced molecule Chapter You must understand chemistry to understand life Describe the difference between the terms element and atom What are chemical symbols and what is the periodic table Draw a model of a neutral atom with atomic number and atomic mass and compare with your groupmates Draw a model of a neutral atom with atomic number and atomic mass and compare with your groupmates Then compare with the previous atom that you drew and discuss isotopes What are electron orbitals What is the valence shell How does the valence shell relate to chemical reactivity of an atom As a group draw a Venn diagram for the following terms molecule compound Then place the following in the diagram O NaCl H O Discuss moles atomic mass units and Avogadro s number Why use moles instead of just mass Discuss the water and glucose problem What is a covalent bond What do polar and nonpolar mean for covalent bonds Give an example of each What are ions What are cations and anions What is an ionic bond Give an example What are hydrogen bonds Draw an example Discuss the chemical equations in the notes and the terms there reactant product equilibrium What is a redox reaction and how does it relate to movement of electrons and movement of energy What gets oxidized reduced in the following making NaCl rusting iron What gains loses energy in each case Overview In many ways life can be viewed as a complicated chemical reaction Modern models of how life works at all levels typically have at least some aspect of chemistry as a major component or underpinning Elements and Atoms elements substances that cannot be further broken down into other substances at least by ordinary chemical reactions every element has a chemical symbol H for hydrogen O for oxygen etc this is most familiar from the periodic table there are naturally occurring elements from hydrogen up to uranium elements O C H N make about of the mass of most living things others are consistently present in small amounts in living things Ca P K S Na Mg Cl Fe several others are typically found only in trace amounts trace elements these tend to vary considerably in amount and even presence depending on the type of organism an atom is the smallest unit of an element that still retains the properties of that element atoms consist of subatomic particles electron - contributes no significant mass to the atom but carries a - electrical charge proton - contributes a mass of approximately mass unit and carries a electrical charge neutron - contributes a mass of approximately mass unit and carries no net electrical charge protons and neutrons are found in the nucleus center of an atom elements differ from each other because they contain different numbers of protons all hydrogen atoms contain proton all carbon atoms contain protons all oxygen atoms contain protons etc atomic number number of protons in the nucleus the periodic table has elements arranged largely according to atomic number protons neutrons determine atomic mass each contribute atomic mass unit amu or Dalton atoms that have the same number of protons but have different numbers of neutrons therefore different masses are referred to as isotopes atomic nuclei can undergo changes decay some elements are more stable than others some isotopes are more stable than others most unstable radioisotopes decay rates are statistical averages used for measuring time passage in many areas of science carbon dating etc the radiation emitted upon decay alpha beta and or gamma can be used as a tool for experiments can also be used medically has other uses and dangers nuclear power nuclear bombs radiation poisoning etc radiation can cause mutations in DNA can interfere with cell division electrons occupy orbitals surrounding the nucleus and move at the speed of light because ATOMS are electrically neutral the number of electrons an atom has always equals the number of protons electrons can exist at different energy levels which correspond to orbitals the further away an orbital carries an electron from the nucleus the higher the energy level of the electron electrons with similar energies make up an electron shell the outer electron s are known as the valence electron s collectively they occupy the valence shell the chemical properties of an atom are largely determined by the valence electrons the science of chemistry mostly involves study of how electrons move about the nucleus store energy and determine chemical properties of substances as a result Describing Atomic Combinations atoms combine to form molecules and compounds molecule two or more atoms held together by covalent bonds defined later may be composed of one or more elements examples O H O not all substances are molecular NaCl table salt isn t if a substance is molecular then an individual molecule is the smallest unit of the substance that exhibits the properties of the substance thus a molecule differs in its physical and chemical properties from the elements that make it up compound - a specific combination of two or more different elements chemically combined in a fixed ratio compounds have unique physical and chemical properties that differ from those of the elements used to make it some compounds are held together by covalent bonds and are therefore molecular some are held together by ionic bonds defined later chemists use two types of formulas to describe substances chemical formula - a shorthand formula showing the number of atoms of each element present in a molecule often called molecular formula if a molecule is involved examples H O CO O C H O follows simplest ratio for ionic substances NaCl etc structural formula - shows the arrangement of atoms in a molecule examples water H O H carbon dioxide O C O molecular oxygen O O the number of units of a substance are described using the mole molecular mass is the sum of the atomic masses of the atoms in the molecule since the actual mass of an atom is extremely small it is convenient in the real world to work with a large number of atoms at the same time The amount of a substance that in grams has the same number as the atomic mass is a mole Thus water has molecular mass a mole of water has a mass of g The mole is simply a conversion factor from the small scale of atomic mass units to the more familiar gram scale the factor represents the number of units molecules or atoms in a mole this factor called Avogadro s number is x atoms or molecules Chemical Bonds Hold Molecules Together and Store Energy recall that electrons in the outermost shell of an atom valence electrons determine the chemical behavior of the atom i e what type and how many chemical bonds it can readily form most atoms in biological systems seek to have electrons in their outermost shell hydrogen seeks to have or electrons in its outermost shell since atoms have the same number of electrons as protons they meet this need to have a full valence shell by sharing giving up or acquiring electrons from other atoms this forms chemical bonds a chemical bond is a reduced energy state bond energy is the amount of energy required to break a particular chemical bond there are two principle types of strong chemical bonds covalent bonds - electrons are shared between two atoms ionic bonds - one atom completely gives up an electron to another atom covalent bonds result in filled valence shells electrons are shared in pairs a single electron pair shared a single covalent bond double and triple covalent bonds are also possible carbon forms covalent bonds covalent bonds give molecules definite shapes the shared atomic orbitals require definite spatial arrangements that depend on the atoms involved in the bond covalent bonds can be nonpolar equal sharing of electrons or polar unequal sharing of electrons polar bonds result if one nucleus holds a stronger attraction on the electron pair molecules with polar bonds polar molecules have regions with partial charges ionic bonds when an atom gains or gives up one or more electrons it is called an ion cations - ions that have lost one or more electrons have a positive charge anions - ions that have gained one or more electrons have a negative charge the suffix ide indicates an anion polyatomic ions can also form covalently bound atoms that lose or gain electrons or protons only polyatomic ions can lose or gain protons polyatomic cations positive charge polyatomic anions negative charge an ionic bond is formed by the attraction between a cation and an anion an ionic compound is a substance held together by ionic bonds ionic compounds dissociate into individual ions when dissolved in a polar substance such as water hydration surrounding the ions with the ends water molecules with the opposite partial charge hydrogen bonds weak interactions involving partially charged hydrogen atoms the interaction is with another atom with a partial - charge can be within the same large molecule or between molecules hydrogen bonds are common and important in living things water forms hydrogen bonds because they are weak hydrogen bonds are relatively easy to manipulate collectively hydrogen bonds can be very strong they hold together the two strands of DNA for example In aqueous systems such as living organisms the typical relative bond strengths are covalent bond ionic bond hydrogen bond Chemical Equations Describe Chemical Reactions Reactants are written on the left Products are written on the right an arrow is used to show the direction the reaction proceeds C H O O CO H O Energy double arrows of equal lengths indicate equilibrium reactions reactions proceeding simultaneously at equal rates in both directions N H NH Sometimes different lengths of double arrows are used to indicate which direction is favored CO H O H CO Oxidation-Reduction Reactions redox reactions Are Common in Biological Systems oxidation is a chemical process in which an atom molecule or ion loses an electron s reduction is the opposite an electron is gained charge is reduced oxidation and reduction are always paired hence redox reactions example rusting when iron rusts iron oxide is formed by the oxidation of iron this can be described by a chemical reaction as shown below Fe O Fe O during the process iron atoms Fe become iron ions Fe Fe Fe e- therefore we can say that iron atoms were oxidized to produce iron ions above on the flip side the oxygen atoms gain electrons we can say that the oxygen is reduced in the reaction O e- O - oxygen is the most common oxidizing agent hence the general term oxidation in biological systems typically molecules are oxidized and reduced very important in many processes such as photosynthesis respiration electrons are less easily lost from molecules than from atoms molecules typically will lose the equivalent of a complete hydrogen atom when oxidized this means that both a proton and an electron are removed from the oxidized molecule and may be added to the reduced molecule thus counting charge changes is not sufficient for analyzing redox reactions look for movement of electrons in redox reactions involving biological molecules Chapter Water and the fitness of the environment What s so great about water Overview Life as we know it requires water All organisms that we know of are made mostly of liquid water and most of their metabolism requires an aqueous medium In addition many organisms live in liquid water or in an environment dominated by water in its various states solid liquid or gas Some numbers cells are typically or more water by mass about of the Earth s surface is covered by liquid water But then just being common on the Earth doesn t make something essential for life A large percentage of the Earth s crust is sand but we don t consider sand a requirement for life What is it about water that makes it so special The chemistry of water is dominated by the polar nature of water molecules oxygen atoms are electron seeking electronegative especially compared to hydrogen thus for an oxygen-hydrogen bond the oxygen atom has a partial - charge the hydrogen atoms have a partial charge the polar character of water allows water molecules to form many up to hydrogen bonds What properties of water are important for life four properties of water are critical for life as we know it and all of them come in some way from water s polar nature and the resulting tendency of water to form hydrogen bonds and similar interactions water is the principal solvent in living things water exhibits both cohesive and adhesive forces water helps maintain a stable temperature ice solid water floats in liquid water water is the principal solvent in living things the highly polar character of water makes it an excellent solvent for other polar substances and for ionic compounds hydrophilic substances interact readily with water water does not readily dissolve nonpolar hydrophobic substances thus hydrophobic substances are good components for membranes water exhibits both cohesive and adhesive forces due to hydrogen bonding cohesive forces are caused by the attraction of water molecules to other water molecules and give water a high surface tension the ability of a water surface to withstand some stress adhesive forces cause water molecules to be attracted to other kinds of molecules it is how things are made wet capillary action the tendency of water to move up narrow tubes even against gravity results from cohesion and adhesion living organisms take advantage of this water helps maintain a stable temperature the unusual specific heat of water leads to temperature stability specific heat - the amount of energy required to raise the temperature of a specific amount of a substance one degree Celsius for water calorie heat needed for g of water to raise by one degree Celsius the specific heat of water is much higher than most other substances due to hydrogen bonding as a comparison the specific heat of sand is about calories for g thus it requires the gain or loss of more energy heat to change the temperature of water than it does other substances since much of the ecosphere is water and most biological organisms are more than water this property of water leads to temperature stability which is critical for most living organisms the high heat of vaporization of water helps cool the ecosphere and biological organisms heat of vaporization is the amount of heat energy required to convert one gram of liquid into the gaseous state because of hydrogen bonds in liquid water water has an extremely high heat of vaporization a commonly used unit for measuring energy is the calorie the amount of heat energy required to cause the temperature of one gram of pure water to rise one degree Celsius calories are required to convert one gram of liquid water into water vapor biological organisms take advantage of this property of water to cool themselves examples sweating and cooling a leaf ice floats ice is less dense than liquid water liquid water like most substances becomes denser as it cools but only up to a point at C under standard atmospheric pressure water begins to expand as it cools further that is it gets less dense from then on due to hydrogen bonds becoming locked in place at C ice freezes into a crystal based on the placement of hydrogen bonds floating ice keeps lakes etc from freezing solid and is important for temperature cycling on the planet Acids and Bases acids are proton donors an acid is a substance that dissociates in solution to yield hydrogen ions H HA an acid H A- an anion note that hydrogen has an atomic number of which means that the nucleus has only one proton when the atom loses its electron to become a hydrogen ion all that remains is the proton thus hydrogen ions are sometimes referred to as protons therefore any substance that yields a proton is an acid or an acid is a proton donor bases are proton acceptors a base is a substance that can accept a proton bases either dissociate in water to produce hydroxide ions and a cation or split water to form a cation and hydroxide ion NaOH Na OH- or B a base HOH BH OH- water tends to slightly dissociate into hydrogen and hydroxide ions H and OH- HOH H OH- in pure water the concentrations of these ions are equal H OH- - M note that the designation M stands for molar the moles of a substance per liter of solution the product of these remains constant H x OH- - acidic solutions have an elevated H and thus reduced OH- basic solutions have an elevated OH- and thus reduced H the pH scale is a convenient short hand notation to express the proton concentration of a solution the pH of a solution is defined as the reciprocal of the logarithm of the proton concentration in the solution or -log H pure water having a proton concentration of - M has pH a pH below is acidic and a pH above is basic the pH of most living cells is usually around to buffers minimize pH changes weak acids and weak bases serve as buffers living things use buffers to prevent dramatic changes in pH which can kill them carbonate bicarbonate is an example of a biologically important buffer system CO H O H CO H HCO - because these reactions are equilibrium reactions as H is added to this system bicarbonate HCO - and protons are consumed to keep the proton concentration constant pH constant producing H CO if OH- ions are added to the system H ions are consumed forming water More H ions are produced by the dissociation of H CO to form protons and bicarbonate This demonstrates how the pH is stabilized as acid or base is added Some useful definitions solvent a liquid into which a substance dissolves solute the dissolved substance solution solvent solute salts form from acids and bases water is formed the cation of the base and the anion of the acid form the salt HCl NaOH NaCl HOH electrolytes are salts acids or bases that form ions in water and thus can conduct an electrical current when dissolved in water pure water is a poor conductor of electricity but put in a salt and it becomes an excellent conductor nonelectrolytes are substances like sugar that dissolve in water but do not become ionic mixtures - a mixture of or more elements and or compounds they can be broken down into elements and compounds by simple physical means There are two types heterogeneous mixtures - mixtures that are not of uniform composition throughout - a living organism is a good example homogeneous mixtures - mixtures that are completely uniform throughout - a salt water solution is a good example Chapter What s so great about water Draw a water molecule structural formula and then draw in four more around it that are connected to it by hydrogen bonds List and describe at least four properties of water that result from its polar nature hydrogen bonds Describe how water acts as a temperature buffer creates temperature stability Define acids and bases What does pH stand for and how does the pH scale work How do pH buffers work Overview Life as we know it requires water All organisms that we know of are made mostly of liquid water and most of their metabolism requires an aqueous medium In addition many organisms live in liquid water or in an environment dominated by water in its various states solid liquid or gas Some numbers cells are typically or more water by mass about of the Earth s surface is covered by liquid water But then just being common on the Earth doesn t make something essential for life A large percentage of the Earth s crust is sand but we don t consider sand a requirement for life What is it about water that makes it so special The chemistry of water is dominated by the polar nature of water molecules oxygen atoms are electron seeking electronegative especially compared to hydrogen thus for an oxygen-hydrogen bond the oxygen atom has a partial - charge the hydrogen atoms have a partial charge the polar character of water allows water molecules to form many up to hydrogen bonds What properties of water are important for life four properties of water are critical for life as we know it and all of them come in some way from water s polar nature and the resulting tendency of water to form hydrogen bonds and similar interactions water is the principal solvent in living things water exhibits both cohesive and adhesive forces water helps maintain a stable temperature ice solid water floats in liquid water water is the principal solvent in living things the highly polar character of water makes it an excellent solvent for other polar substances and for ionic compounds hydrophilic substances interact readily with water water does not readily dissolve nonpolar hydrophobic substances thus hydrophobic substances are good components for membranes water exhibits both cohesive and adhesive forces due to hydrogen bonding cohesive forces are caused by the attraction of water molecules to other water molecules and give water a high surface tension the ability of a water surface to withstand some stress adhesive forces cause water molecules to be attracted to other kinds of molecules it is how things are made wet capillary action the tendency of water to move up narrow tubes even against gravity results from cohesion and adhesion living organisms take advantage of this water helps maintain a stable temperature the unusual specific heat of water leads to temperature stability specific heat - the amount of energy required to raise the temperature of a specific amount of a substance one degree Celsius for water calorie heat needed for g of water to raise by one degree Celsius the specific heat of water is much higher than most other substances due to hydrogen bonding as a comparison the specific heat of sand is about calories for g thus it requires the gain or loss of more energy heat to change the temperature of water than it does other substances since much of the ecosphere is water and most biological organisms are more than water this property of water leads to temperature stability which is critical for most living organisms the high heat of vaporization of water helps cool the ecosphere and biological organisms heat of vaporization is the amount of heat energy required to convert one gram of liquid into the gaseous state because of hydrogen bonds in liquid water water has an extremely high heat of vaporization a commonly used unit for measuring energy is the calorie the amount of heat energy required to cause the temperature of one gram of pure water to rise one degree Celsius calories are required to convert one gram of liquid water into water vapor biological organisms take advantage of this property of water to cool themselves examples sweating and cooling a leaf ice floats ice is less dense than liquid water liquid water like most substances becomes denser as it cools but only up to a point at C under standard atmospheric pressure water begins to expand as it cools further that is it gets less dense from then on due to hydrogen bonds becoming locked in place at C ice freezes into a crystal based on the placement of hydrogen bonds floating ice keeps lakes etc from freezing solid and is important for temperature cycling on the planet Acids and Bases acids are proton donors an acid is a substance that dissociates in solution to yield hydrogen ions H HA an acid H A- an anion note that hydrogen has an atomic number of which means that the nucleus has only one proton when the atom loses its electron to become a hydrogen ion all that remains is the proton thus hydrogen ions are sometimes referred to as protons therefore any substance that yields a proton is an acid or an acid is a proton donor bases are proton acceptors a base is a substance that can accept a proton bases either dissociate in water to produce hydroxide ions and a cation or split water to form a cation and hydroxide ion NaOH Na OH- or B a base HOH BH OH- water tends to slightly dissociate into hydrogen and hydroxide ions H and OH- HOH H OH- in pure water the concentrations of these ions are equal H OH- - M note that the designation M stands for molar the moles of a substance per liter of solution the product of these remains constant H x OH- - acidic solutions have an elevated H and thus reduced OH- basic solutions have an elevated OH- and thus reduced H the pH scale is a convenient short hand notation to express the proton concentration of a solution the pH of a solution is defined as the reciprocal of the logarithm of the proton concentration in the solution or -log H pure water having a proton concentration of - M has pH a pH below is acidic and a pH above is basic the pH of most living cells is usually around to buffers minimize pH changes weak acids and weak bases serve as buffers living things use buffers to prevent dramatic changes in pH which can kill them carbonate bicarbonate is an example of a biologically important buffer system CO H O H CO H HCO - because these reactions are equilibrium reactions as H is added to this system bicarbonate HCO - and protons are consumed to keep the proton concentration constant pH constant producing H CO if OH- ions are added to the system H ions are consumed forming water More H ions are produced by the dissociation of H CO to form protons and bicarbonate This demonstrates how the pH is stabilized as acid or base is added Some useful definitions solvent a liquid into which a substance dissolves solute the dissolved substance solution solvent solute salts form from acids and bases water is formed the cation of the base and the anion of the acid form the salt HCl NaOH NaCl HOH electrolytes are salts acids or bases that form ions in water and thus can conduct an electrical current when dissolved in water pure water is a poor conductor of electricity but put in a salt and it becomes an excellent conductor nonelectrolytes are substances like sugar that dissolve in water but do not become ionic mixtures - a mixture of or more elements and or compounds they can be broken down into elements and compounds by simple physical means There are two types heterogeneous mixtures - mixtures that are not of uniform composition throughout - a living organism is a good example homogeneous mixtures - mixtures that are completely uniform throughout - a salt water solution is a good example Chapter Carbon and the molecular diversity of life Life is based on molecules with carbon organic molecules Much of the chemistry of life is based on organic compounds organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen the chemistry of organic molecules is organized around the carbon atom carbon atoms have six electrons - in level and in their valence outer shell level Carbon is not a strongly electron seeking element and it does not readily give up its electrons Thus carbon does not readily from ionic bonds It almost always shares electrons forming covalent bonds carbon can form up to covalent bonds and typically does form all four wide diversity in organic compounds over million identified variety partially because carbon tends to bond to carbon hydrogen oxygen nitrogen sulfur and phosphorus hydrocarbons contain only hydrogen and carbon single carbon-carbon bonds allow rotation around them and lend flexibility in molecules building of organic macromolecules also leads to diversity carbon works well as a molecular backbone for forming long chain molecules due to the number and strength of its bonds particularly carbon-carbon bonds stronger carbon-carbon bonds can be made with double and triple covalent bonds carbon chains can branch the shape of a molecule is important in determining its chemical and biological properties the bonds formed by carbon are formed at degree angles from each other and form a pyramid with a triangular base called a tetrahedron when double bonds are formed the bonds are formed at angles degrees apart and they all lie in the same plane These bond angles for carbon play a critical role in determining the shape of molecules generally there is freedom to rotate around carbon to carbon single bonds but rotation around double bonds is not permitted Isomers are molecules that have the same molecular formula but different structures there are two kinds of isomers structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms example ethanol and dimethyl ether C H O stereoisomers - substances with the same arrangement of covalent bonds but the order in which the atoms are arranged in space is different two important types for our use cis-trans isomers associated with compounds that have carbon-carbon double bonds since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in relationship to each other larger items together cis larger item opposite trans examples trans- -butene and cis- -butene enantiomers substances that are mirror images of each other and that cannot be superimposed on each other sometimes called optical isomers typically only one form of an enatiomer is found and or used by organisms the enantiomers are given designations such as - vs - or D- vs L- or R - vs S - biologically important enantiomers include amino acids found in proteins most are L-amino acids e g L-leucine L-alanine etc sugars most are D-sugars e g D-glucose D-fructose etc Functional groups determine most of the reactive properties functions of organic molecules functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond the properties of the major classes of organic compounds carbohydrates lipids proteins and nucleic acids are determined mostly by their functional groups learn these seven functional groups note X here stands for the rest of the molecule hydroxyl group X-OH polar found in alcohols carbonyl group X-C O polar found in aldehydes and ketones carboxyl group X-COOH weakly acidic found in organic acids such as amino acids amino groups X-NH weakly basic found in such things as amino acids sulfhydryl groups X-SH essentially nonpolar found in some amino acids phosphate groups X-PO H weakly acidic found in such things as phospholipids and nucleic acids methyl groups X-CH nonpolar thus hydrophobic found in such things as lipids other membrane components Chapter Life is based on molecules with carbon organic molecules Discuss the chemistry of carbon How does it typically bond What does it typically bond to What sort of shapes angles freedoms etc are associated with the bonds that it makes Draw a tetrahedron Discuss isomers What are they What is the difference between structural isomers and stereoisomers Between cis-trans isomers and enantiomers Draw an example of each of these structural isomers cis-trans isomers enantiomers What is a functional group and why is it useful to know them Quiz each other on the names and chemistry of the functional groups in the notes Chapter Life is based on molecules with carbon organic molecules Much of the chemistry of life is based on organic compounds organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen the chemistry of organic molecules is organized around the carbon atom carbon atoms have six electrons - in level and in their valence outer shell level Carbon is not a strongly electron seeking element and it does not readily give up its electrons Thus carbon does not readily from ionic bonds It almost always shares electrons forming covalent bonds carbon can form up to covalent bonds and typically does form all four wide diversity in organic compounds over million identified variety partially because carbon tends to bond to carbon hydrogen oxygen nitrogen sulfur and phosphorus hydrocarbons contain only hydrogen and carbon single carbon-carbon bonds allow rotation around them and lend flexibility to molecules building of organic macromolecules also leads to diversity carbon works well as a molecular backbone for forming long chain molecules due to the number and strength of its bonds particularly carbon-carbon bonds stronger carbon-carbon bonds can be made with double and triple covalent bonds carbon chains can branch the shape of a molecule is important in determining its chemical and biological properties the bonds formed by carbon are formed at degree angles from each other and form a pyramid with a triangular base called a tetrahedron when double bonds are formed the bonds are formed at angles degrees apart and they all lie in the same plane These bond angles for carbon play a critical role in determining the shape of molecules generally there is freedom to rotate around carbon to carbon single bonds but rotation around double bonds is not permitted Isomers are molecules that have the same molecular formula but different structures there are two kinds of isomers structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms example ethanol and dimethyl ether C H O stereoisomers - substances with the same arrangement of covalent bonds but the order in which the atoms are arranged in space is different two important types for our use cis-trans isomers associated with compounds that have carbon-carbon double bonds since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in relationship to each other larger items together cis larger items opposite trans examples trans- -butene and cis- -butene enantiomers substances that are mirror images of each other and that cannot be superimposed on each other sometimes called optical isomers typically only one form of an enatiomer pair is found in and or used by organisms the enantiomers are given designations such as - vs - or D- vs L- or R - vs S - biologically important enantiomers include amino acids found in proteins most are L-amino acids e g L-leucine L-alanine etc sugars most are D-sugars e g D-glucose D-fructose etc Functional groups determine most of the reactive properties functions of organic molecules functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond the properties of the major classes of organic compounds carbohydrates lipids proteins and nucleic acids are determined mostly by their functional groups learn these seven functional groups note X here stands for the rest of the molecule hydroxyl group X-OH polar found in alcohols carbonyl group X-C O polar found in aldehydes and ketones carboxyl group X-COOH weakly acidic found in organic acids such as amino acids amino group X-NH weakly basic found in such things as amino acids sulfhydryl group X-SH essentially nonpolar found in some amino acids phosphate group X-PO H weakly acidic found in such things as phospholipids and nucleic acids methyl group X-CH nonpolar thus hydrophobic found in such things as lipids other membrane components Chapter The structure and function of macromolecules What are the major types of organic molecules many biological molecules are polymers polymers are long chains or branching chains based on repeating subunits monomers example proteins the polymer are made from amino acids the monomers example nucleic acids the polymer are made from nucleotides the monomers very large polymers hundreds of subunits or more are called macromolecules polymers are degraded into monomers by hydrolysis break with water typically requires an enzyme to occur at a decent rate hydrogen from water is attached to one monomer and a hydroxyl from water is attached to the other monomers are covalently linked to form polymers by condensation also typically requires an enzyme to occur at a decent rate typically the equivalent of a water molecule is removed dehydration synthesis The four major classes of biologically important organic molecules are carbohydrates lipids proteins or polypeptides and related compounds and nucleic acids and related compounds carbohydrates include sugars starches and cellulose carbohydrates contain only the elements carbon hydrogen and oxygen the ratio works out so that carbohydrates are typically CH O n carbohydrates are the main molecules in biological systems created for energy storage and consumed for energy production some are also used as building materials grouped into monosaccharides disaccharides and polysaccharides monosaccharides are simple sugars a single monomer have or carbons referred to as trioses tetroses pentoses hexoses and heptoses examples of pentoses include ribose and deoxyribose part of nucleic acids examples of hexoses include glucose fructose and galactose glucose is most abundant Examine the structural formulas for glucose fructose and galactose Note that they are all isomers of each other i e they have the chemical formula C H O Glucose and galactose are structural isomers of fructose while glucose and galactose are diastereomers a type of stereoisomer pentose and hexose sugars actually form ring structures in solution this often creates diastereomers example -glucose and -glucose note how carbons are given numbers to indicate position disaccharides consist of two monosaccharide units the two monomers are joined by a glycosidic linkage or glycosidic bond formed when the equivalent of a water molecule is removed from the two monosaccharides an oxygen atom is bound to a carbon from each momomer typically the linkage is between carbon of one and of the other maltose sucrose and lactose are common disaccharides maltose malt sugar has two glucose subunits sucrose table sugar glucose fructose lactose milk sugar glucose galactose polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds number of subunits varies typically thousands can be branched or unbranched some are easily broken down and are good for energy storage examples starch glycogen some are harder to break down and are good as structural components example cellulose starch is the main storage carbohydrate of plants polymer made from -glucose units linked primarily between carbons and amylose unbranched starch chain only have - linkages amylopectin branched starch chain branches by linkages between carbons and plants store starches in organelles called amyloplasts a type of plastid glycogen is the main storage carbohydrate of animals similar to starch but very highly branched and more water-soluble is NOT stored in an organelle mostly found in liver and muscle cells cellulose is the major structural component of most plant cell walls polymer made from -glucose units linked primarily between carbons and similar to starch but note that the - linkage makes a huge difference unlike starch most organisms cannot digest cellulose cellulose is a major constituent of cotton wood and paper cellulose contains of the carbon in found in plants fibrous cellulose is the fiber in your diet some fungi bacteria and protozoa make enzymes that can break down cellulose animals that live on materials rich in cellulose e g cattle sheep and termites contain microorganisms in their gut that are able to break down cellulose for use by the animal carbohydrates can be modified from the basic CH O n formula many modified carbohydrates have important biological roles example chitin structural component in fungal cell walls and arthropod exoskeletons example galactosamine in cartilage example glycoproteins and glycolipids in cellular membranes lipids are fats and fat-like substances lipids are a heterogeneous group of compounds defined by solubility not structure oily or fatty compounds lipids are principally hydrophobic and are relatively insoluble in water some do have polar and nonpolar regions lipids consist mainly of carbon and hydrogen some oxygen and or phosphorus mainly in the polar regions of lipids that have such regions roles of lipids include serving as membrane structural components as signaling molecules and as energy storage molecules major classes of lipids that you need to know are triacylglycerols fats phospholipids and terpenes triacylglycerols contain glycerol joined to three fatty acids glycerol is a three carbon alcohol with -OH groups a fatty acid is a long unbranched hydrocarbon chain carboxyl group at one end saturated fatty acids contain no carbon-carbon double bonds usually solid at room temp unsaturated fatty acids contain one or more double bonds usually liquid at room temp monounsaturated one double bond polyunsaturated more than one double bond about different fatty acids are commonly found in triacylglycerols most have an even number of carbons condensation results in an ester linkage between a fatty acid and the glycerol one attached fatty acid monoacylglycerol two diacylglycerol three triacylglycerol triacylglycerols also called triglycerides are the most abundant lipids and are important sources of energy phospholipids consist of a diacylglycerol molecule a phosphate group esterified to the third -OH group of glycerol and an organic molecule usually charged or polar esterified to the phosphate phospholipids are amphipathic they have a nonpolar end the two fatty acids and a polar end the phosphate and organic molecule this is often drawn with a polar head and two nonpolar tails the nonpolar or hydrophobic portion of the molecule tends to stay away from water and the polar or hydrophilic portion of the molecule tends to interact with water because of this character phospholipids are important constituents of biological membranes terpenes are long-chained lipids built from -carbon isoprene units many pigments such as chlorophyll carotenoids and retinal are terpenes or modified terpenes often called terpenoids other terpenes terpenoids include natural rubber and essential oils such as plant fragrances and many spices steroids are terpene derivatives that contain four rings of carbon atoms side chains extend from the rings length and structure of the side chains varies one type of steroid cholesterol is an important component of cell membranes other examples many hormones such as testosterone estrogens proteins are macromolecules that are polymers formed from amino acids monomers proteins have great structural diversity and perform many roles roles include enzyme catalysis defense transport structure support motion regulation protein structure determines protein function proteins are polymers made of amino acid monomers linked together by peptide bonds amino acids consist of a central or alpha carbon bound to that carbon is a hydrogen atom an amino group -NH a carboxyl group -COOH and a variable side group R group the R group determines the identity and much of the chemical properties of the amino acid there are amino acids that commonly occur in proteins pay attention to what makes an R group polar nonpolar or ionic charged and thus their hydrophobic or hydrophilic nature most amino acids have enantiomers when this is so the amino acids found in proteins are nearly always of the L-configuration plants and bacteria can usually make their own amino acids many animals must obtain some amino acids from their diet essential amino acids the peptide bond joins the carboxyl group of one amino acid to the amino group of another is formed by a condensation reaction two amino acids fastened together by a peptide bond is called a dipeptide several amino acids fastened together by peptide bonds are called a polypeptide the sequence of amino acids determine the structure and thus the properties of a protein proteins have levels of organization or structure primary structure of a protein is the sequence of amino acids in the peptide chain secondary structure of a protein results from hydrogen bonds involving the backbone where the peptide chain is held in structures either a coiled -helix or folded -pleated sheet proteins often have both types of secondary structure in different regions of the chain tertiary structure of a protein is the overall folded shape of a single polypeptide chain determined by secondary structure combined with interactions between R groups NOTE book defines this in a confusing way use my way quaternary structure of a protein results from interactions between two or more separate polypeptide chains the interactions are of the same type that produce and structure in a single polypeptide chain when present structure is the final three-dimensional structure of the protein the protein conformation example hemoglobin has polypeptide chains not all proteins have structure ultimately the secondary tertiary and quaternary structures of a protein derive from its primary structure but molecular chaperones may aid the folding process protein conformation determines function denaturation is unfolding of a protein disrupting and structure changes in temperature pH or exposure to various chemicals can cause denaturation denatured proteins typically cannot perform their normal biological function denaturation is generally irreversible enzymes are biological substances that regulate the rates of the chemical reactions in living organisms most enzymes are proteins covered in some detail later in this course related compounds amino acids modified amino acids polypeptides too short to be considered true proteins and modified short polypeptides nucleic acids transmit hereditary information by determining what proteins a cell makes two classes of nucleic acids found in cells deoxyribonucleic acid DNA and ribonucleic acid RNA DNA carries the genetic information cells use to make proteins RNA functions in protein synthesis according to mechanisms we will discuss later in the semester nucleic acids are polymers made of nucleotide monomers a nucleotide consists of a five-carbon sugar ribose or deoxyribose one or more phosphate groups and a nitrogenous base an organic ring compound that contains nitrogen purines are double-ringed nitrogenous bases pyrimidines are single-ringed nitrogenous bases DNA typically contains the purines adenine A and guanine G and the pyrimidines cytosine C and thymine T RNA typically contains the purines adenine A and guanine G and the pyrimidines cytosine C and uracil U nucleotides are fastened together by phosphodiester bonds the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide the joining is yet another condensation reaction the way that the are joined creates a polynucleotide strand with and ends the sequence of the bases fastened to the sugar-phosphate backbone is genetic information DNA is typically a double stranded molecule the two strands twist into a double helix hydrogen bonds between the nitrogenous bases of opposite strands hold the strands together the two strands are antiparallel RNA is typically a single stranded nucleic acid molecule having only a single polynucleotide chain related compounds nucleotides modified nucleotides dinucleotides some single and double nucleotides with important biological functions adenosine triphosphate ATP is an important energy carrying compound in metabolism cyclic adenosine monophosphate cAMP is a hormone intermediary compound nicotinamide adenine dinucleotide NAD is an electron carrier which is oxidized or reduced in many metabolic reactions Chapter What are the major types of organic molecules Discuss hydrolysis and condensation and the connection between them Carbohydrates what are they and what are they used for What terms are associated with them including the monomers and the polymer bond name Give some examples of molecules in this group Lipids what are they and what are they used for What terms are associated with them including major classes and bond names Give some examples of molecules in this group Polypeptides what are they and what are they used for What terms are associated with them including the monomers and the polymer bond name Give some examples of molecules in this group Discuss how to tell which of these categories an amino acid falls into hydrophobic or hydrophilic and within the hydrophilic polar or charged Discuss the four levels of protein structure Nucleic acids what are they and what are they used for What terms are associated with them including the monomers and the polymer bond name Give some examples of molecules in this group What are and ends What does antiparallel mean in DNA What are ATP cAMP and NAD What are their roles in cells Chapter What are the major types of organic molecules many biological molecules are polymers polymers are long chains or branching chains based on repeating subunits monomers example proteins the polymer are made from amino acids the monomers example nucleic acids the polymer are made from nucleotides the monomers very large polymers hundreds of subunits or more are called macromolecules polymers are degraded into monomers by hydrolysis break with water typically requires an enzyme to occur at a decent rate hydrogen from water is attached to one monomer and a hydroxyl from water is attached to the other monomers are covalently linked to form polymers by condensation also typically requires an enzyme to occur at a decent rate typically the equivalent of a water molecule is removed dehydration synthesis The four major classes of biologically important organic molecules are carbohydrates lipids proteins or polypeptides and related compounds and nucleic acids and related compounds carbohydrates include sugars starches and cellulose carbohydrates contain only the elements carbon hydrogen and oxygen the ratio works out so that carbohydrates are typically CH O n carbohydrates are the main molecules in biological systems created for energy storage and consumed for energy production some are also used as building materials grouped into monosaccharides disaccharides and polysaccharides monosaccharides are simple sugars a single monomer have or carbons referred to as trioses tetroses pentoses hexoses and heptoses examples of pentoses include ribose and deoxyribose part of nucleic acids examples of hexoses include glucose fructose and galactose glucose is most abundant Examine the structural formulas for glucose fructose and galactose Note that they are all isomers of each other i e they have the chemical formula C H O Glucose and galactose are structural isomers of fructose while glucose and galactose are diastereomers a type of stereoisomer pentose and hexose sugars actually form ring structures in solution this often creates diastereomers example -glucose and -glucose note how carbons are given numbers to indicate position disaccharides consist of two monosaccharide units the two monomers are joined by a glycosidic linkage or glycosidic bond formed when the equivalent of a water molecule is removed from the two monosaccharides an oxygen atom is bound to a carbon from each momomer typically the linkage is between carbon of one and of the other maltose sucrose and lactose are common disaccharides maltose malt sugar has two glucose subunits sucrose table sugar glucose fructose lactose milk sugar glucose galactose polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds number of subunits varies typically thousands can be branched or unbranched some are easily broken down and are good for energy storage examples starch glycogen some are harder to break down and are good as structural components example cellulose starch is the main storage carbohydrate of plants polymer made from -glucose units linked primarily between carbons and amylose unbranched starch chain only have - linkages amylopectin branched starch chain branches by linkages between carbons and plants store starches in organelles called amyloplasts a type of plastid glycogen is the main storage carbohydrate of animals similar to starch but very highly branched and more water-soluble is NOT stored in an organelle mostly found in liver and muscle cells cellulose is the major structural component of most plant cell walls polymer made from -glucose units linked primarily between carbons and similar to starch but note that the - linkage makes a huge difference unlike starch most organisms cannot digest cellulose cellulose is a major constituent of cotton wood and paper cellulose contains of the carbon in found in plants fibrous cellulose is the fiber in your diet some fungi bacteria and protozoa make enzymes that can break down cellulose animals that live on materials rich in cellulose e g cattle sheep and termites contain microorganisms in their gut that are able to break down cellulose for use by the animal carbohydrates can be modified from the basic CH O n formula many modified carbohydrates have important biological roles example chitin structural component in fungal cell walls and arthropod exoskeletons example galactosamine in cartilage example glycoproteins and glycolipids in cellular membranes lipids are fats and fat-like substances lipids are a heterogeneous group of compounds defined by solubility not structure oily or fatty compounds lipids are principally hydrophobic and are relatively insoluble in water some do have polar and nonpolar regions lipids consist mainly of carbon and hydrogen some oxygen and or phosphorus mainly in the polar regions of lipids that have such regions roles of lipids include serving as membrane structural components as signaling molecules and as energy storage molecules major classes of lipids that you need to know are triacylglycerols fats phospholipids and terpenes triacylglycerols contain glycerol joined to three fatty acids glycerol is a three carbon alcohol with -OH groups a fatty acid is a long unbranched hydrocarbon chain carboxyl group at one end saturated fatty acids contain no carbon-carbon double bonds usually solid at room temp unsaturated fatty acids contain one or more double bonds usually liquid at room temp monounsaturated one double bond polyunsaturated more than one double bond about different fatty acids are commonly found in triacylglycerols most have an even number of carbons condensation results in an ester linkage between a fatty acid and the glycerol one attached fatty acid monoacylglycerol two diacylglycerol three triacylglycerol triacylglycerols also called triglycerides are the most abundant lipids and are important sources of energy phospholipids consist of a diacylglycerol molecule a phosphate group esterified to the third -OH group of glycerol and an organic molecule usually charged or polar esterified to the phosphate phospholipids are amphipathic they have a nonpolar end the two fatty acids and a polar end the phosphate and organic molecule this is often drawn with a polar head and two nonpolar tails the nonpolar or hydrophobic portion of the molecule tends to stay away from water and the polar or hydrophilic portion of the molecule tends to interact with water because of this character phospholipids are important constituents of biological membranes terpenes are long-chained lipids built from -carbon isoprene units many pigments such as chlorophyll carotenoids and retinal are terpenes or modified terpenes often called terpenoids other terpenes terpenoids include natural rubber and essential oils such as plant fragrances and many spices steroids are terpene derivatives that contain four rings of carbon atoms side chains extend from the rings length and structure of the side chains varies one type of steroid cholesterol is an important component of cell membranes other examples many hormones such as testosterone estrogens proteins are macromolecules that are polymers formed from amino acids monomers proteins have great structural diversity and perform many roles roles include enzyme catalysis defense transport structure support motion regulation protein structure determines protein function proteins are polymers made of amino acid monomers linked together by peptide bonds amino acids consist of a central or alpha carbon bound to that carbon is a hydrogen atom an amino group -NH a carboxyl group -COOH and a variable side group R group the R group determines the identity and much of the chemical properties of the amino acid there are amino acids that commonly occur in proteins pay attention to what makes an R group polar nonpolar or ionic charged and thus their hydrophobic or hydrophilic nature most amino acids have enantiomers when this is so the amino acids found in proteins are nearly always of the L-configuration plants and bacteria can usually make their own amino acids many animals must obtain some amino acids from their diet essential amino acids the peptide bond joins the carboxyl group of one amino acid to the amino group of another is formed by a condensation reaction two amino acids fastened together by a peptide bond is called a dipeptide several amino acids fastened together by peptide bonds are called a polypeptide the sequence of amino acids determine the structure and thus the properties of a protein proteins have levels of organization or structure primary structure of a protein is the sequence of amino acids in the peptide chain secondary structure of a protein results from hydrogen bonds involving the backbone where the peptide chain is held in structures either a coiled -helix or folded -pleated sheet proteins often have both types of secondary structure in different regions of the chain tertiary structure of a protein is the overall folded shape of a single polypeptide chain determined by secondary structure combined with interactions between R groups NOTE book defines this in a confusing way use my way quaternary structure of a protein results from interactions between two or more separate polypeptide chains the interactions are of the same type that produce and structure in a single polypeptide chain when present structure is the final three-dimensional structure of the protein the protein conformation example hemoglobin has polypeptide chains not all proteins have structure ultimately the secondary tertiary and quaternary structures of a protein derive from its primary structure but molecular chaperones may aid the folding process protein conformation determines function denaturation is unfolding of a protein disrupting and structure changes in temperature pH or exposure to various chemicals can cause denaturation denatured proteins typically cannot perform their normal biological function denaturation is generally irreversible enzymes are biological substances that regulate the rates of the chemical reactions in living organisms most enzymes are proteins covered in some detail later in this course related compounds amino acids modified amino acids polypeptides too short to be considered true proteins and modified short polypeptides nucleic acids transmit hereditary information by determining what proteins a cell makes two classes of nucleic acids found in cells deoxyribonucleic acid DNA and ribonucleic acid RNA DNA carries the genetic information cells use to make proteins RNA functions in protein synthesis according to mechanisms we will discuss later in the semester nucleic acids are polymers made of nucleotide monomers a nucleotide consists of a five-carbon sugar ribose or deoxyribose one or more phosphate groups and a nitrogenous base an organic ring compound that contains nitrogen purines are double-ringed nitrogenous bases pyrimidines are single-ringed nitrogenous bases DNA typically contains the purines adenine A and guanine G and the pyrimidines cytosine C and thymine T RNA typically contains the purines adenine A and guanine G and the pyrimidines cytosine C and uracil U nucleotides are fastened together by phosphodiester bonds the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide the joining is yet another condensation reaction the way that the are joined creates a polynucleotide strand with and ends the sequence of the bases fastened to the sugar-phosphate backbone is genetic information DNA is typically a double stranded molecule the two strands twist into a double helix hydrogen bonds between the nitrogenous bases of opposite strands hold the strands together the two strands are antiparallel RNA is typically a single stranded nucleic acid molecule having only a single polynucleotide chain related compounds nucleotides modified nucleotides dinucleotides some single and double nucleotides with important biological functions adenosine triphosphate ATP is an important energy carrying compound in metabolism cyclic adenosine monophosphate cAMP is a hormone intermediary compound nicotinamide adenine dinucleotide NAD is an electron carrier which is oxidized or reduced in many metabolic reactions Chapter A tour of the Cell Cell theory All living organisms are composed of cells smallest building blocks of all multicellular organisms all cells are enclosed by a surface membrane that separates them from other cells and from their environment specialized structures with the cell are called organelles many are membrane-bound Today all new cells arise from existing cells All presently living cells have a common origin all cells have basic structural and molecular similarities all cells share similar energy conversion reactions all cells maintain and transfer genetic information in DNA the genetic code is essentially universal Cell organization and homeostasis Plasma membrane surrounds cells and separates their contents from the external environment Cells are heterogeneous mixtures with specialized regions and structures such as organelles Cell size is limited surface area to volume ratio puts a limit on cell size food and or other materials must get into the cell waste products must be removed from the cell thus cells need a high surface area to volume ratio but volume increases faster than surface area as cells grow larger cell shape varies depending both on function and surface area requirements Studying cells microscopy and fractionation Most cells are large enough to be resolved from each other with light microscopes LM cells were discovered by Robert Hooke in he saw the remains of cell walls in cork with a LMs at about x magnification modern LMs can reach up to x LM resolution clarity is limited to about m due to the wavelength of visible light thus only about times better than the human eye even at maximum magnification small cells such as most bacteria are about m across just on the edge of resolution some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases Resolution of most subcellular structure requires electron microscopy EM electrons have a much smaller wavelength than light resolve down to under nm magnification up to x or more and resolution over times better than the human eye includes transmission TEM and scanning SEM forms transmission - electron passes through sample need very thin samples nm or less thick samples embedded in plastic and sliced with a diamond knife scanning samples are gold-plated electrons interact with the surface images have a -D appearance Cells can be broken and fractionated to separate cellular components for study cells are broken lysed by disrupting the cell membrane often using some sort of detergent grinding and other physical force may be required especially if cell walls are present centrifugation is used to separate cellular components using a centrifuge samples are spun at high speeds resulting in exposure to a centrifugal force of thousands to hundreds of thousands times gravity example x G results in a pellet and supernatant cell components will be in one or the other depending on their individual properties intact membrane-bound organelles often wind up in pellets depending on their density and the centrifugal force reached more dense more likely in pellet special treatments can determine whether a component ends up in the pellet or supernatant density gradients can also be used to subdivide pellet components based on their density this can be used to separate organelles from each other for example Golgi apparatus from ER Eukaryotic vs prokaryotic cells eukaryotic cells have internal membranes and a distinct membrane-enclosed nucleus typically - m in diameter prokaryotic cells do not have internal membranes thus no nuclear membrane main DNA molecule chromosome is typically circular its location is called the nuclear area other small DNA molecules plasmids are often present found throughout the cell plasma membrane is typically enclosed in a cell wall often the cell wall is enclosed in an outer envelope or outer membrane do not completely lack organelles the plasma membrane and ribosomes are both present and are considered organelles AKA bacteria prokaryotic cells are typically - m in diameter Compartments in eukaryotic cells cell regions organelles two general regions inside the cell cytoplasm and nucleoplasm cytoplasm everything outside the nucleus and within the plasma membrane contains fluid cytosol and organelles nucleoplasm everything within the nuclear membrane membranes separate cell regions have nonpolar regions that help form a barrier between aqueous regions allow for some selection in what can cross a membrane more details later nucleus the control center of the cell typically large m and singular nuclear envelope double membrane surrounding the nucleus nuclear pores protein complexes that cross both membranes and regulate passage chromatin DNA-protein complex have granular appearance easily stained for microscopy chrom- color unpacked DNA kept ready for message transcription and DNA replication proteins protect DNA and help maintain structure and function chromosomes condensed or packed DNA ready for cell division -some body nucleoli regions of ribosome subunit assembly appears different due to high RNA and protein concentration no membrane ribosomal RNA rRNA transcribed from DNA there proteins imported from cytoplasm join with rRNA at a nucleolus to from ribosome subunits ribosome subunits are exported to the cytoplasm through nuclear pores ribosomes the sites of protein synthesis ribosomes are granular bodies with three RNA strands and about associated proteins two main subunits large and small perform the enzymatic activity for forming peptide bonds and serve as the sites of translation of genetic information into protein sequences prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes in eukaryotes the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm some are free in the cytoplasm while others are associated with the endoplasmic reticulum ER endomembrane system a set of membranous organelles that interact with each other via vesicles includes ER Golgi apparatus vacuoles lysosomes microbodies and in some definitions the nuclear membrane and the plasma membrane endoplasmic reticulum ER membrane network that winds through the cytoplasm winding nature of the ER provides a lot of surface area many important cell reactions or sorting functions require ER membrane surface ER lumen internal aqueous compartment in ER separated from the rest of the cytosol typically continuous throughout ER and with the lumen between the nuclear membranes enzymes within lumen and imbedded in lumen side of ER differ from those on the other side thus dividing the functional regions smooth ER primary site of lipid synthesis many detoxification reactions and sometimes other activities rough ER ribosomes that attach there insert proteins into the ER lumen as they are synthesized ribosome attachment directed by a signal peptide at the amino end of the polypeptide see Ch p a protein RNA signal recognition particle SRP binds to the signal peptide and pauses translation at the ER the assembly binds to an SRP receptor protein SRP leaves protein synthesis resumes now into the ER lumen and the signal peptide is cut off proteins inserted into the ER lumen may be membrane bound or free proteins are often modified in the lumen example carbohydrates or lipids added proteins are transported from the ER in transport vesicles vesicles small membrane-bound sacs buds off of an organelle ER or other contents within the vesicles often proteins transported to another membrane surface vesicles fuses with membranes delivering contents to that organelle or outside of the cell Golgi apparatus AKA Golgi complex a stack of flattened membrane sacs cisternae where proteins further processed modified and sorted the post office of the cell not contiguous with ER and lumen of each sac is usually separate from the rest has three areas cis medial and trans cis face near ER and receives vesicles from it current model cisternal maturation model holds that vesicles actually coalesce to continually form new cis cisternae medial region as a new cis cisterna is produced the older cisternae mature and move away from the ER in this region proteins are further modified making glycoproteins and or lipoproteins where appropriate and maturing cisternae may make other products for example many polysaccharides are made in the Golgi some materials are needed back a the new cis face and are transported there in vesicles trans face nearest to the plasma membrane a fully matured cisterna breaks into many vesicles that are set up to go to the proper destination such as the plasma membrane or another organelle taking their contents with them lysosomes small membrane-bound sacs of digestive enzymes serves to confine the digestive enzymes and their actions allows maintenance of a better pH for digestion often about pH formed by budding from the Golgi apparatus special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome used to degrade ingested material or in some cases dead or damaged organelles ingested material is found in vesicles that bud in from the plasma membrane the complex molecules in those vesicles is then digested can also fuse with dead or damaged organelles and digest them digested material can then be sent to other parts of the cell for use found in animals protozoa debatable in other eukaryotes but all must have something like a lysosome vacuoles large membrane-bound sacs that perform diverse roles have no internal structure distinguished from vesicles by size in plants algae and fungi performs many of the roles that lysosomes perform for animals central vacuole typically a single large sac in plant cells that can be of the cell volume usually formed from fusion of many small vacuoles in immature plant cells storage sites for water food salts pigments and metabolic wastes important in maintaining turgor pressure tonoplast membrane of the plant vacuole food vacuoles present in most protozoa and some animal cells usually bud from plasma membrane and fuse with lysosomes for digestion contractile vacuoles used by many protozoa for removing excess water microbodies small membrane-bound organelles that carry out specific cellular functions examples lysosomes could be consider a type of microbody peroxisomes sites of many metabolic reactions that produce hydrogen peroxide H O which is toxic to the rest of the cell peroxisomes have enzymes to break down H O protecting the cell peroxisomes are abundant in liver cells in animals and leaf cells in plants normally found in all eukaryotes example detoxification of ethanol in liver cells occurs in peroxisomes glyoxysomes in plant seeds contains enzymes that convert stored fats into sugar energy converting organelles energy obtained from the environment is typically chemical energy in food or light energy mitochondria are the organelles where chemical energy is placed in a more useful molecule and chloroplasts are plastids where light energy is captured during photosynthesis mitochondria the site of aerobic respiration recall aerobic respiration sugar oxygen carbon dioxide water energy the energy is actually stored in ATP mitochondria have a double membrane space between membranes intermembrane space inner membrane is highly folded forming cristae provides a large surface area inner membrane is also a highly selective barrier the enzymes that conduct aerobic respiration are found in the inner membrane inside of inner membrane is the matrix analogous to the cytoplasm of a cell mitochondria have their own DNA and are inherited from the mother only in humans mitochondria have their own division process similar to cell division each cell typically has many mitochondria which can only arise from mitochondrial division some cells require more mitochondria than others mitochondria can leak electrons into the cell allowing toxic free radicals to form mitochondria play a role in initiating apoptosis programmed cell death plastids organelles of plants and algae that produce and store food include amyloplasts for starch storage chromoplasts for color often found in petals and fruits and chloroplasts for photosynthesis like mitochondria have their own DNA typically a bit larger and more disk-shaped than mitochondria however derive from undifferentiated proplastids although role of mature plastids can sometimes change numbers and types of plastids vary depending on the organism and the role of the cell chloroplasts get their green color from chlorophyll the main light harvesting pigments involved in photosynthesis carbon dioxide water light energy food glucose oxygen chloroplasts have a double membrane the region within the inner membrane is the stroma it is analogous to the mitochondrial matrix inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are grouped in stacks called grana the thylakoids enclose aqueous regions called the thylakoid lumen chlorophyll is found in the thylakoid membrane and the reactions of photosynthesis take place there and in the stroma carotenoids in the chloroplast serve as accessory pigments for photosynthesis endosymbiont theory states that mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost their independence the cells containing the endosymbionts became dependent upon them for food processing and in turn provide them with a protected and rich environment a mutualistic relationship supporting evidence the size scale is right - mitochondria and plastids are on the high end of the size of typical bacteria endosymbionts also have their own DNA and their own cell division in many ways they act like bacterial cells the DNA sequence and arrangement circular chromosomes of endosymbionts is closer to that of bacteria than to that found in the eukaryotic nucleus endosymbionts have their own ribosomes which are much like bacterial ribosomes the genetic code used by endosymbionts is more like that of bacteria than of eukaryotes there are other known more modern endosymbiotic relationships algae in corals bacteria within protozoans in termite guts some genes appear to have been shuttled out of the endosymbionts to the nucleus many of the proteins used by endosymbionts are actually encoded by nuclear genes and translated in the cytoplasm or on rough ER and transported to the endosymbionts DNA sequencing of endosymbionts is being used to trace the evolutionary history of the endosymbionts appears that endosymbiosis began about to billion years ago around when the first eukaryotic cells appeared mitochondria appear to have a monophyletic origin one initial endosymbiotic event giving rise to all mitochondria in eukaryotic cells today plastids appear to have a polyphyletic origin several initial endosymbiotic events giving rise to different plastid lines present today in algae and plants some argue that endosymbionts were simply derived within the early eukaryotic cells along with the nuclear membrane and the proliferation of other membrane surfaces common in eukaryotes but not prokaryotes Cytoskeleton eukaryotic cells typically have a size and shape that is maintained the cytoskeleton is a dense network of protein fibers that provides needed structural support the network also has other functions a scaffolding for organelles cell movement and cell division dynamic nature to the protein fibers is involved here transport of materials within the cell the cytoskeleton is composed of three types of protein filaments microtubules microfilaments and intermediate filaments microtubules are the thickest filaments of the cytoskeleton hollow rod -shaped cylinders about nm in diameter made of -tubulin and -tubulin dimers dimers can be added or removed from either end dynamic nature one end plus end adds dimers more rapidly than the minus end can be anchored where an end is attached to something and can no longer add or lose dimers microtubule-organizing centers MTOCs serve as anchors centrosome in animal cells centrosome has two centrioles in a perpendicular arrangement centrioles have a x structure sets of attached microtubules forming a hollow cylinder centrioles are duplicated before cell division play an organizing role for microtubule spindles in cell division other eukaryotes must use some alternative MTOC during cell division still incompletely described microtubules are involved in moving organelles motor proteins such as kinesin and dynein attach to organelle and to microtubule using ATP as an energy source the motor proteins change shape and thus produce movement microtubule essentially acts as a track for the motor protein motor proteins are directional kinesin moves toward the plus end dynein away from it cilia and flagella are made of microtubules thin flexible projections from cells used in cell movement or to move things along the cell surface share the same basic structure called cilia if short - m typically and flagella if long typically m central stalk covered by cell membrane extension and anchored to a basal body stalk has two inner microtubules surrounded by nine attached pairs of microtubules arrangement dynein attached to the outer pairs actually fastens the pair to its neighboring pair dynein motor function causes relative sliding of filaments this produces bending movement of the cilium or flagellum the basal body is very much like the centriole has a x structure replicates itself microfilaments are solid filaments about nm in diameter composed of two entwined chains of actin monomers linker proteins cross-link the actin chains with each other and other actin associated proteins actin monomers can be added to lengthen the microfilament or removed to shorten it this can be used to generate movement important in muscle cells in conjunction with myosin they are responsible for muscle contraction also associate with myosin in many cells to form contractile structures such as used in cell division intermediate filaments typically just a bit wider than microfilaments this is the catch-all group for cytoskeletal filaments composed of a variety of other proteins the types of proteins involved differ depending on cell types and on the organism apparently limited to animal cells and protozoans not easily disassembled thus more permanent a web of intermediate filaments reinforces cell shape and positions of organelles they give structural stability prominent in cells that withstand mechanical stress form the most insoluble part of the cell Outside the cell Most prokaryotes have a cell wall an outer envelope and a capsule capsule is also called glycocalyx or cell coat Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it plants have thick defined cell walls made primarily of cross-linked cellulose fibers growing plant cells secrete a primary cell wall which is thin and flexible after a plant cell stops growing the primary cell wall is usually thickened and solidified or a secondary cell wall is produced between the primary cell wall and the plasma membrane secondary cell walls still contain cellulose but typically have other material as well that strengthens them further for example lignin in wood fungi typically have thinner cell walls than plants made primarily of cross-linked chitin fibers animals do not have cell walls but their cells secrete varying amounts of compounds that can produce a glycocalyx and an extracellular matrix ECM glycocalyx polysaccharides attached to proteins and lipids on the outer surface of the plasma membrane typically functions in cell recognition and communication cell contacts and structural reinforcement often works through direct interaction with the ECM ECM a gel of carbohydrates and fibrous proteins several different molecules can be involved main structural protein is tough fibrous collagen fibronectins are glycoproteins in the ECM that often bind to both collagen and integrins integrins are proteins in the plasma membrane that typically receive signals from the ECM Specialized contacts junctions between cells cell junctions typically connect cells and can allow special transport between connected cells A anchoring junctions hold cells tightly together one common type in animals is the desmosome desmosomes form strong bonds between cytoskeletons of adjacent cells and hold them together materials can still pass in the space between cells with anchoring junctions NOT involved in the transport of materials between cells tight junctions between some animal cells are used to seal off body cavities cell plasma membranes are adjacent to each other and held together by a tight seal materials cannot pass between cells held together by tight junctions NOT involved in the transport of materials between cells gap junctions between animal cells act as selective pores proteins connect the cells those proteins are grouped in cylinders of subunits the cylinder can be opened to form a small pore less than nm through which small molecules can pass plasmodesmata act as selective pores between plant cells plant cell walls perform the functions of tight junctions and desmosomes plant cell walls form a barrier to cell-to-cell communication that must be breached by the functional equivalent of a gap junction plasmodesmata are relatively wide channels - nm across the cell wall between adjacent cells they actually connect the plasma membranes of the two cells and allow exchange of some materials between the cells Chapter A Tour of the Cell What are the main tenets of cell theory What are the major lines of evidence that all presently living cells have a common origin What is surface area to volume ratio and why is it an important consideration for cells What usually happens to surface area to volume ratio as cells grow larger Compare and contrast LM and EM SEM and TEM Include the terms resolution and magnification in your discussions Describe cell fractionation Why is it done and how is it done Include the terms lyse centrifugation pellet and supernatant in your discussion How do prokaryotic cells and eukaryotic cells differ from each other in typical size and general organization Describe cytoplasm cytosol nucleoplasm and the general role of membranes in cells List as many organelles as you can think of Describe their structures and key functions Draw and label a typical animal cell and a typical plant cell including organelles Describe the nuclear envelope nuclear pores chromatin chromosomes and nucleoli in terms of structures and key functions Name something that you KNOW must get out of the nucleus for cells to function Describe the structure and function of ribosomes What is the endomembrane system include organelle components Diagram and describe the pathway from synthesis to final destination for a secreted protein Then do the same for a plasma membrane protein Diagram the cisternal maturation model for the Golgi Describe the structure and function of ER vesicles vacuoles Golgi apparatus microbodies in general lysosomes peroxisomes glyoxysomes Draw a mitochondrion in cross-section and describe its structure and functions Draw a chloroplast in cross-section and describe its structure and functions Describe the endosymbiont theory Include evidence for it including predictions that have proven true What are the functions of the cytoskeleton What are the three main types of cytoskeleton Describe the structure and function s of each type Describe the structure and function s of motor proteins MTOCs centrosomes centrioles cilia and flagella Describe the outer part and outside interface of a typical prokaryotic cell typical plant cell typical fungal cell typical animal cell Diagram and describe the animal cell glycocalyx and ECM interaction include collagen fibronectin and integrin Chapter A Tour of the Cell Cell theory All living organisms are composed of cells smallest building blocks of all multicellular organisms all cells are enclosed by a surface membrane that separates them from other cells and from their environment specialized structures with the cell are called organelles many are membrane-bound Today all new cells arise from existing cells All presently living cells have a common origin all cells have basic structural and molecular similarities all cells share similar energy conversion reactions all cells maintain and transfer genetic information in DNA the genetic code is essentially universal Cell organization and homeostasis Plasma membrane surrounds cells and separates their contents from the external environment Cells are heterogeneous mixtures with specialized regions and structures such as organelles Cell size is limited surface area to volume ratio puts a limit on cell size food and or other materials must get into the cell waste products must be removed from the cell thus cells need a high surface area to volume ratio but volume increases faster than surface area as cells grow larger cell shape varies depending both on function and surface area requirements Studying cells microscopy and fractionation Most cells are large enough to be resolved from each other with light microscopes LM cells were discovered by Robert Hooke in he saw the remains of cell walls in cork with a LM at about x mag modern LMs can reach up to x LM resolution clarity is limited to about m due to the wavelength of visible light only about times better than the human eye even at maximum magnification small cells such as most bacteria are about m across just on the edge of resolution some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases Resolution of most subcellular structure requires electron microscopy EM electrons have a much smaller wavelength than light resolve down to under nm magnification up to x or more and resolution over times better than the human eye includes transmission TEM and scanning SEM forms transmission - electron passes through sample need very thin samples nm or less thick samples embedded in plastic and sliced with a diamond knife scanning samples are gold-plated electrons interact with the surface images have a -D appearance Cells can be broken and fractionated to separate cellular components for study cells are broken lysed by disrupting the cell membrane often using some sort of detergent grinding and other physical force may be required especially if cell walls are present centrifugation is used to separate cellular components using a centrifuge samples are spun at high speeds resulting in exposure to a centrifugal force of thousands to hundreds of thousands times gravity example x G results in a pellet and supernatant cell components will be in one or the other depending on their individual properties intact membrane-bound organelles often wind up in pellets depending on their density and the centrifugal force reached more dense more likely in pellet special treatments can determine whether a component ends up in the pellet or supernatant density gradients can also be used to subdivide pellet components based on their density this can be used to separate organelles from each other for example Golgi apparatus from ER Eukaryotic vs prokaryotic cells eukaryotic cells have internal membranes and a distinct membrane-enclosed nucleus typically - m in diameter prokaryotic cells do not have internal membranes thus no nuclear membrane main DNA molecule chromosome is typically circular its location is called the nuclear area other small DNA molecules plasmids are often present found throughout the cell plasma membrane is usually enclosed in a cell wall that is often covered with a capsule layer of proteins and or sugars do not completely lack organelles the plasma membrane and ribosomes are both present and are considered organelles AKA bacteria prokaryotic cells are typically - m in diameter Compartments in eukaryotic cells cell regions organelles two general regions inside the cell cytoplasm and nucleoplasm cytoplasm everything outside the nucleus and within the plasma membrane contains fluid cytosol and organelles nucleoplasm everything within the nuclear membrane membranes separate cell regions have nonpolar regions that help form a barrier between aqueous regions allow for some selection in what can cross a membrane more details later nucleus the control center of the cell typically large m and singular nuclear envelope double membrane surrounding the nucleus nuclear pores protein complexes that cross both membranes and regulate passage chromatin DNA-protein complex have granular appearance easily stained for microscopy chrom- color unpacked DNA kept ready for message transcription and DNA replication proteins protect DNA and help maintain structure and function chromosomes condensed or packed DNA ready for cell division -some body nucleoli regions of ribosome subunit assembly appears different due to high RNA and protein concentration no membrane ribosomal RNA rRNA transcribed from DNA there proteins imported from cytoplasm join with rRNA at a nucleolus to from ribosome subunits ribosome subunits are exported to the cytoplasm through nuclear pores ribosomes the sites of protein synthesis ribosomes are granular bodies with three RNA strands and about associated proteins two main subunits large and small perform the enzymatic activity for forming peptide bonds serve as the sites of translation prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes in eukaryotes the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm some are free in the cytoplasm while others are associated with the endoplasmic reticulum ER endomembrane system a set of membranous organelles that interact with each other via vesicles includes ER Golgi apparatus vacuoles lysosomes microbodies and in some definitions the nuclear membrane and the plasma membrane endoplasmic reticulum ER membrane network that winds through the cytoplasm winding nature of the ER provides a lot of surface area many important cell reactions or sorting functions require ER membrane surface ER lumen internal aqueous compartment in ER separated from the rest of the cytosol typically continuous throughout ER and with the lumen between the nuclear membranes enzymes within lumen and imbedded in lumen side of ER differ from those on the other side thus dividing the functional regions smooth ER primary site of lipid synthesis many detoxification reactions and sometimes other activities rough ER ribosomes that attach there insert proteins into the ER lumen as they are synthesized ribosome attachment directed by a signal peptide at the amino end of the polypeptide see Ch p a protein RNA signal recognition particle SRP binds to the signal peptide and pauses translation at the ER the assembly binds to an SRP receptor protein SRP leaves protein synthesis resumes now into the ER lumen and the signal peptide is cut off proteins inserted into the ER lumen may be membrane bound or free proteins are often modified in the lumen example carbohydrates or lipids added proteins are transported from the ER in transport vesicles vesicles small membrane-bound sacs buds off of an organelle ER or other contents within the vesicles often proteins transported to another membrane surface vesicles fuses with membranes delivering contents to that organelle or outside of the cell Golgi apparatus AKA Golgi complex a stack of flattened membrane sacs cisternae where proteins further processed modified and sorted the post office of the cell not contiguous with ER and lumen of each sac is usually separate from the rest has three areas cis medial and trans cis face near ER and receives vesicles from it current model cisternal maturation model holds that vesicles actually coalesce to continually form new cis cisternae medial region as a new cis cisterna is produced the older cisternae mature and move away from the ER in this region proteins are further modified making glycoproteins and or lipoproteins where appropriate and maturing cisternae may make other products for example many polysaccharides are made in the Golgi some materials are needed back a the new cis face and are transported there in vesicles trans face nearest to the plasma membrane a fully matured cisterna breaks into many vesicles that are set up to go to the proper destination such as the plasma membrane or another organelle taking their contents with them lysosomes small membrane-bound sacs of digestive enzymes serves to confine the digestive enzymes and their actions allows maintenance of a better pH for digestion often about pH formed by budding from the Golgi apparatus special sugar attachments to hydrolytic enzymes made in the ER target them to the lysosome used to degrade ingested material or in some cases dead or damaged organelles ingested material is found in vesicles that bud in from the plasma membrane the complex molecules in those vesicles is then digested can also fuse with dead or damaged organelles and digest them digested material can then be sent to other parts of the cell for use found in animals protozoa debatable in other eukaryotes but all must have something like a lysosome vacuoles large membrane-bound sacs that perform diverse roles have no internal structure distinguished from vesicles by size in plants algae and fungi performs many of the roles that lysosomes perform for animals central vacuole typically a single large sac in plant cells that can be of the cell volume usually formed from fusion of many small vacuoles in immature plant cells storage sites for water food salts pigments and metabolic wastes important in maintaining turgor pressure tonoplast membrane of the plant vacuole food vacuoles present in most protozoa and some animal cells usually bud from plasma membrane and fuse with lysosomes for digestion contractile vacuoles used by many protozoa for removing excess water microbodies small membrane-bound organelles that carry out specific cellular functions examples lysosomes could be consider a type of microbody peroxisomes sites of many metabolic reactions that produce hydrogen peroxide H O which is toxic to the cell peroxisomes have enzymes to break down H O protecting the cell peroxisomes are abundant in liver cells in animals and leaf cells in plants normally found in all eukaryotes example detoxification of ethanol in liver cells occurs in peroxisomes glyoxysomes in plant seeds contains enzymes that convert stored fats into sugar energy converting organelles energy obtained from the environment is typically chemical energy in food or light energy mitochondria are the organelles where chemical energy is placed in a more useful molecule and chloroplasts are plastids where light energy is captured during photosynthesis mitochondria the site of aerobic respiration recall aerobic respiration sugar oxygen carbon dioxide water energy the energy is actually stored in ATP mitochondria have a double membrane space between membranes intermembrane space inner membrane is highly folded forming cristae provides a large surface area inner membrane is also a highly selective barrier the enzymes that conduct aerobic respiration are found in the inner membrane inside of inner membrane is the matrix analogous to the cytoplasm of a cell mitochondria have their own DNA and are inherited from the mother only in humans mitochondria have their own division process similar to cell division each cell typically has many mitochondria which can only arise from mitochondrial division some cells require more mitochondria than others mitochondria can leak electrons into the cell allowing toxic free radicals to form mitochondria play a role in initiating apoptosis programmed cell death plastids organelles of plants and algae that produce and store food include amyloplasts for starch storage chromoplasts for color often found in petals and fruits and chloroplasts for photosynthesis like mitochondria have their own DNA typically a bit larger and more disk-shaped than mitochondria however derive