Biology notes for Exam 1
Biology notes for Exam 1 Biol 1103k
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This 38 page Study Guide was uploaded by Megan Smith on Tuesday February 2, 2016. The Study Guide belongs to Biol 1103k at Georgia State University taught by David blaustein in Summer 2015. Since its upload, it has received 133 views. For similar materials see Introductory biology I in Biology at Georgia State University.
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Date Created: 02/02/16
CHAPTER 1.1 – WHAT IS LIFE 1.1 WHAT IS LIFE Biology • Comes from the Greek root “bio” meaning “life” and “logy” meaning “the study of”. i. Life if defined as: a. Organisms acquire and use materials and energy b. Organisms actively maintain organized complexity c. Organisms perceive and respond to stimuli d. Organisms grow e. Organisms reproduce f. Organisms, collectively, have the capacity to evolve Hint: use page 3 to try to explain how the water flea has the properties of life ii. Cell • The basic unit of life iii. Parts of a cell a. Membrane (plasma membrane) – separates the cell form its surroundings. b. Nucleus – suspended within a fluid environment c. Cell Wall - outer most layer B. Organisms Acquire and Use Materials and Energy i. The Energy that sustains life comes from the sunlight ii. Photosynthesis • Photosynthetic organisms trap and store energy for their own use • Energy stored in their bodies also powers all other forms of life C. Organisms Actively maintain Organized Complexity i. homeostasis • Organisms maintain relatively constant internal conditions D. Organisms Perceive and Respond to Stimuli i. Organisms sense and respond to internal and external environmental stimuli ii. Sensory organs in animals can detect and respond to external stimuli such as light, sound, chemicals, etc. iii. Plants and bacteria also respond to stimuli • Ex. Plants grow towards light E. Organisms grow i. All organisms become larger overtime ii. Growth requires organism obtain material and energy from the outside world F. Organisms Reproduce i. Reproduction happens in a variety of ways a. Dividing in half b. Producing seeds c. Bearing live young d. Laying eggs ii. Offspring inherit instructions from their parents for producing and maintaining their particular forms of life called deoxyribonucleic acid (DNA) G. Organisms, collectively, have the capacity to evolve i. Evolution • The process by which modern organisms have descended from earlier and different forms of life • Resulted from changes in DNA within populations ii. Population • A group of the same type of organism inhabiting the same area 2 1.2 WHAT IS EVOLUTION Evolution • Explains why Earth has such a huge diversity of life • Accounts for the remarkable similarities among different types of organisms A. Three Natural Processes Underlie Evolution i. Evolution is an automatic and inevitable outcome of three natura l occurrences a. Differences in DNA among members of a population b. Inheritances of these differences by their offspring c. Natural selection i. The increased ability of offspring that inherit certain forms and combinations of DNA molecules to survive and reproduce B. Mutations are the Original Source of Difference in DNA i. Genes • Segments of DNA • the basic units of heredity • before a cell divides, all of its DNA must be copied so its genes can be passed along ii. Mutations • cells sometimes make errors while copying • results from damaged DNA o ultraviolet rays from sunlight o toxic chemicals from cigarette smoke C. Some mutations are inherited • Helps offspring to survive and reproduce more successfully than those lacking the mutation i. Some Inherited Mutations Help Individuals Survive and Reproduce • Natural Selection o Organisms with certain inherited traits survive and reproduce better than others in a given environment • Adaptions o Structures, physiological processes, or behaviors that help an organism to survive and reproduce in a particular environment o Help organisms escape predators, capture prey, reach sunlight, or accomplish other feats that help ensure their survival and reproduction • Extinction 3 o The complete elimination of a form of li fe 1.3 HOW DO SCIENTISTS ST UDY LIFE ? A. Life can be studied at Different Levels i. Elements • Substances that can not be broken down or converted to simpler substances ii. Atom • The smallest particle of an element that retains all the properties of that element iii. Example of Element and Atom • A diamond is a form of the element carbon • The smallest possible unit of a diamond is an individual carbon atom iv. Molecule • Atoms may combine in specific ways to form molecules o Example: one oxygen atom can combine with two hydrogen atoms to form a molecule of water v. Tissues • Cells of a similar types may combine to form tissues in multicellular organisms • Different types of tissues, in turn, unite to form functional units called organs (such as the entire stomach) vi. Organ System • The grouping of two or more organs that work together to perform a specific body function • Combine within complex multicellular organism to carry out the activities of life vii. Levels of organization also extend to groups of organisms a. Atom (smallest) b. Molecule c. Cell d. Tissue e. Organ f. Organ System g. Multicellular organism h. Population i. Species 4 j. Community k. Ecosystem l. Biosphere (largest) viii. Population • A group of organisms of the same type (the same species) that live in a well defined area where they can interact and interbreed with one another ix. Species • Consists of all organisms that are similar enough to interbreed, no matter where they are found x. Community • Formed by populations of different species that live in the same area and interact with one another xi. Ecosystem • Consists of a community and the nonliving environment that surrounds it xii. Biosphere • Includes all life on Earth and the nonliving portions of Earth that support life B. Biologists Classify Organisms Based on Their Evolutionary Relationships i. Domains • Evolutionary relatedness placed animals into three major groups or domains • These classifications reflect fundamental differences among their cell types a. Bacteria b. Archaea c. Eukarya ii. Eukarya • Includes a diverse collection of organism collectively known as protists, and three major subdivisions called King doms iii. Kingdoms a. Fungi b. Plants c. Animals 5 iv. The classification of a given organism into a domain and kingdom is based on three characteristics a. The organisms cell type (simple or complex) b. Whether the organism is unicellular (single cell) or multicellular (composed of many cells) c. How the organism acquired its energy C. Cell type distinguished the Bacteria and Archaea from the Eukarya i. Plasma membrane • Thin sheet of molecules surrounding all cells ii. Organelles • Structures specialized to carry out specific functions such as h elping to synthesize large molecules, digesting food molecules, or obtaining energy. iii. Two fundamentally different types of cells a. Eukaryotic b. Prokaryotic iv. Eukaryotic • Calls are extremely complex and contain a variety of organelles, many of which are surrounded by membranes • All members are composed of eukaryotic cells v. Nucleus • A membrane-enclosed organelle that contains the cell’s DNA vi. Prokaryotic • Cells are far simpler and generally smaller than eukaryotic cells • Lack organelles enclosed by membranes • DNA is not confined in the nucleus • Most abundant forms of life are found in the domains Bacteria and Archaea, which consist entirely of prokaryotic cells D. Multicellularity Occurs Only Among the Eukarya i. Members of the domains Bacteria and Archaea are unicellular ii. Multicellular organisms are found among the Eukarya E. The Eukarya Acquire Energy in Different Ways i. Plants are autotrophs ii. Animals are heterotrophs • Ingest (eat) their own food iii. Fungi are heterotrophic • Absorb their food 6 iv. Autotroph • Self feeding • Acquire their energy through photosynthesis v. Heterotroph • Other feeding • Cannot photosynthesize and so they rely on the bodies of other organisms for food F. Biologists Use the Binomial System to Name Organisms i. The smallest two categories a. Genus b. Species ii. Species • Consists of nearly identical organisms that can interbreed • italicized iii. Genus • Includes many different species with similar characteristics • Capitalized and italicized iv. Binomial System • Provides a unique scientific name for each form of life • Means “two” (bi) “names” (nomial) which consist of the genus and species 1.4 WHAT IS SCIENC E? Science • Systematic inquiry – observation and experiment – into the origins, structure, and behavior of our living and non living surrounding. A. Science is Based on the Principal That All Events Have Natural Causes i. Spontaneous Generation • To believe that life arose spontaneously B. The Scientific Method Is an Important Tool of Scientific Inquiry i. Scientific Method – 6 interrelated items • Begins with an observation of a specific phenomenon • Leads to a question – “What caused this” • After hard thought a hypothesis is formed 7 o A proposed explanation for the phenomenon, often based on limited evidence • Then lead to a prediction o The expected outcome of testing if the hypothesis is correct • Experiments are done to test the hypothesis • A conclusion is reached that either supports or refutes the hypothesis a. Observation b. Question c. Hypothesis d. Prediction e. Experiment f. Conclusion C. Biologists Test Hypotheses Using Controlled Experiments i. Two types of situations are established a. Control Variable ii. Control Situation • All possible variables are held constant iii. Variable • The factor in an experiment that is manipulated to test the hypothesis iv. Valid Scientific Experiment • Must be repeatable by the researcher and by other scientist • The researcher performs multiple repetitions of the experiment v. Francesco Redi’s Experiment • Meat and Flies • Spontaneous Generation? • Page 12 vi. Malte Andersson’s Experiment • Widowbird Tail Feathers • Page 13 D. Scientific Theories Have Been Thoroughly Tested i. Scientific Theory • General and reliable explanation of important natural phenomena that has been developed through extensive and reproducible observations and experiments ii. Natural Law • Best describes a scientific theory 8 • Basic principal derived from the study of nature that has never been disproven by scientific theory iii. Cell Theory • That all living organisms are composed of cells • Fundamental to the principals of Biology E. Scientific Theories Involve Both inductive and Deductive Reasoning i. Inductive Reasoning • Process of creating a broad generalization based on many observations that support it and none that contradict it ii. Deductive reasoning • Starts with a well-supported generalization such as a scientific theory • Uses it to generate hypotheses about how a specific experiment or observation will turn out F. Scientific Theories Are Formulated in Ways That Can Potentially Be Disproved i. Scientists refer to basic principals • These are called “theories” because theories have the potential to be disproved, or falsified G. Science is a Human Endeavor i. Microbiologists • Often study pure cultures • A single type of bacterium grown in sterile, covered dishes free from contamination by other bacteria and molds ii. Fleming’s Culture • became contaminated with a mold (a type of fungus) called Penicillium. • Instead of discarding the dish, Fleming looked at it carefully and observed that no bacteria were growing near the mold • His experiment on page 15 H. Knowledge of Biology Illuminated Life • Some people believe science and new finding rob us of wonder and awe in the world • Example: studying how bee’s pollinate increases out appreciation in the world 9 Date CHAPTER 2 – ATOMS, MOLECULES, AND LIFE A. ATOMS ARE THE BASIC STRUCTURAL UNITS OF ELEMENTS i. Element • A substance that cannot be separated into simpler substances, and cannot be converted into another substance by ordinary chemical reactions • Ex: gold ii. Atom • The smallest unit of an element, and each atom retains all the chem ical properties of that element • Ex: what makes up gold A. Atoms are Composed of Still Smaller Particles iii. Atoms are composed of subatomic particles: a. Neutrons (n) – no charge b. Protons (p+) – single positive charge c. Electrons (e -) – single negative charge • Measured in atomic mass units iv. Mass number • Total number (which equals the total mass) of the protons and neutrons in its nucleus v. Atomic nucleus • Protons and neutrons cluster together in the ce nter of the atom B. Elements are Defined by Their Atomic Number i. Atomic number • Number of protons in the nucleus - called the atomic number - is the feature that defines each element C. Isotopes Are of the Same Element with Different Numbers of Neutrons i. Isotopes • Atoms of the same element with different numbers of neutrons D. Some Isotopes are Radioactive i. Radioactive • Their nuclei spontaneously break apart, or decay. • Radioactive decay emits subatomic particles (such as neutrons) tha t carry large amounts of energy E. Some Radioactive Isotopes Damage Cells • Some radioactive isotopes release particles with enough energy that the can damage DNA, causing mutations. F. Nuclei and Electrons Play Complementary Roles in Atoms i. Nuclei (unless radioactive) provide stability by resistin g disturbances by outside forces ii. Electrons in contrast, are dynamic; they can capture and release energy iii. Electrons form bonds that link atoms together G. Electrons Occupy Complex Regions Around the Nucleus i. Electron shells • Electrons occupy complex three -dimensional regions, called electron shells, around the nucleus • Each shell has a specific energy associated with it • The farther away from the nucleus, the higher the energy of the electrons occupying the shell H. Electrons Can Capture and Release Energy i. Atoms excited by energy, such as light or heat, it can cause an electron to jump from a lower-energy electron shell to a higher -energy electron shell ii. Soon after the electron spontaneously falls back into its original electron shell and releases its extra energy I. As Atomic Number Increases, Electrons Fill Shells Increasingly Distant from the Nucleus i. The shell nearest the nucleus can hold only two ii. The larger more distant shells can hold eight iii. Electrons always fill the most inner shell first iv. Elements with larger num ber of protons in their nuclei require more electrons to balance these protons 2.2 HOW DO ATOMS INTERAC T TO FORM MOLECULES? i. Molecules • Atoms of the same or different elements linked together 2 A. Atoms Form Different Molecules to Fill Vacancies in Their Outer El ectron Shells • Electrons are most stable and less likely to interact with other atoms in the shells that are completely full • Atoms behave generally to two different principals: a. An atom will not react with other atoms when its outermost electron shell is com pletely full. o Such an atom (ex. Helium) is extremely stable and its described as inert o Inert – outermost shell is completely full b. An atom will react with other atoms if its outermost electron shell is only partially full (ex. Hydrogen). o Such an atom is described as reactive o Reactive – not completely full B. Chemical Bonds Hold Atoms Together in Molecules i. Chemical Bonds • Attractive forces that hold atoms together in molecules. • Bonds are formed when reactive atoms gain, lose, ro share electrons to gain stability and become less reactive • Three major types of bonds: a. Ionic b. Covalent c. Hydrogen C. Ionic Bonds Form Among Ions i. When an atom has more electrons than protons it becomes negatively charged ii. When an atom fewer electrons than protons it becomes positively charged iii. When an atom has acquired an overall positive or negative charge it is no longer an atom, but an ion o Ions with opposite charges attract one another o The attraction between positively and negatively charged ions forms ionic bonds iv. Ionic bonds • An electron is TRANSFERED between atoms creating positive and negative ions that attract one another D. Covalent Bonds Form by Sharing Electrons i. Covalent bonds • Atoms with partially full outermost electron shells can become stable by SHARING electrons with one another, filling both of their outer shells and forming covalent bonds. 3 E. Covalent Bonds May Produce Nonpolar or Polar Molecules i. Non polar covalent bonds • Electrons are shared equally between atoms ii. Polar covalent bonds • Electrons are shared unequally between atoms iii. Hydrogen bond • Attractions occur between polar molecules in which H is bonded to O or N • The slightly positive H attracts the slightly negative O or N of a nearby polar molecule iv. Free radicals • Unfilled outer shells • So reactive that the can tear other molecules apart F. Hydrogen Bonds Are Attractive Forces Between Certain Polar Molecules i. Hydrogen Bond • Attraction between a slightly positive hydrogen and slightly negative oxygen or nitrogen located in a nearby molecule or in another part of t he same molecule 2.3 WHY IS WATER SO IMPO RTANT TO LIFE? i. water • Is polar • Hydrogen bonds form among molecules A. Water Molecules Attract One Another i. Hydrogen bonds • Interconnect water molecules • Constantly break and reform allowing water to flow • Cause cohesion o Tendency for molecules of a single type to stick together ii. Cohesion among water molecules produces surface tension • The tendency for a water surface to resist being broken B. Water interact with Many Other Molecules i. Solvent • Substance that dissolves in some othe r substance ii. Solution • A dissolvable substance in a solvent 4 iii. Water dissolves polar molecules because its positive and negative poles are attracted to their oppositely charged poles iv. Hydrophilic • Ions and polar molecules are described as hydrophilic because of t heir electrical attraction for water molecules • Means “water loving” v. Hydrophobic • Larger molecules with nonpolar covalent bonds do not dissolve in water • Means “water-fearing” • Ex: oils and fats vi. Hydrophobic interaction • The tendency of oil molecules to clump to gether in water C. Water Moderates the Effects of Temperature Changes i. Specific heat • The energy required to heat 1 gram of a substance by 1degree C ii. Water has a very high specific heat • Hydrogen bonds need a large amount of heat energy to be broken D. It takes a Lot of Energy to Evaporate Water i. Heat of vaporization • Water has an extremely high heat of vaporization • The amount of heat needed to cause a substance to evaporate o Evaporate – to change from a liquid to a vapor ii. evaporation has a cooling effect because the (warmest) fastest moving molecules are the ones to evaporate…leaving the cool molecules behind E. Water forms an unusual solid: Ice i. Most liquids become denser when they become solid ii. Ice is less dense than liquid water (unusual) iii. Water freeing • Each molecule forms stable hydrogen bonds with four other water molecules • This creates an open, hexagonal (six -sided) arrangement F. Water based solutions can be Acidic, Basic, or Neutral i. Pure water contains equal concentrations of OH - and H+ ii. Acidic • If the concentration of H+ exceeds the concentration of OH - iii. Acid • A substance that releases hydrogen ions when it dissolves in water 5 iv. Basic • If the concentration of OH- is greater than the concentration of H+ v. Base • A substance that combines with hydrogen ions, reducing their number vi. pH Scale • goes 0-14 • measures how acidic or basic a solution is • Neutral pH (equal concentrations of H+ and OH -) is 7 • Acids have a pH below 7 • Pure water has a pH of 7 • Bases have a pH above 7 • Mammals, including humans, have pH in body fluids around 7.4 • Page 31 – examples of each vii. Buffer • Type of molecule that tends to maintain a solution at a constant pH by accepting or releasing H+ in response to small changes in H+ concentration • In the presence of excess H+, a buffer combines with the H+, reducing its concentration • In the presence of excess OH-, buffers release H+, which combines with OH- to form H2O. • THINK: Buffer always reacts with the H+ 6 Date CHAPTER 3 – BIOLOGICAL MOLECULES 3.1 WHY IS CARBON SO IMPORTANT IN BIOLOGI CAL MOLECULES organic • Describes molecules that have a carbon backbone bonded to hydrogen Inorganic • Molecules lack carbon atoms (water and salt) or lack hydrogen atoms (carbon dioxide) • Far less diverse and generally much simpler than organic molecules A. The Unique Bonding Properties of Carbon are Key to the Complexity of Organic Molecules i. Atoms are unstable when their outermost electron shells are only partially filled ii. Depending on the number of vacancies in their shells, two atoms can share two, four, or six electrons o This can form a single, double, or triple covalent bond iii. A carbon atom can become stable by bonding with up to four other atoms or with fewer atoms by formi ng double or even triple bonds o Organic molecules can then assume complex shapes, including branched chains, rings, sheets, or helices. iv. Functional Groups o Commonly occurring combinations of atoms o Less stable than the carbon backbone and more likely to participate in chemical reactions o Table: Important Functional Groups in Biological Molecules 3.2 HOW ARE ORGANIC MOLE CULES SYNTHESIZED? Monomers • Small organic molecules that may bind chemically to other molecules to form polymers Polymers • When small organic molecules join to form longer molecules • Chains of monomers B. Biological Polymers are Formed by Removing Water and Split Apart by Adding Water i. Dehydration synthesis o “removing water put together” o The subunits of large biological molecules are usually joined by a chemical reaction called dehydration synthesis o A hydrogen ion (H+) is removed from one subunit and a hydroxyl ion (OH -) is removed from a second subunit o This leaves openings in the outer el ectron shells of atoms in the two subunits o These openings are filled when the subunits share electrons, creating a covalent bond that links them 2 o The hydrogen ion and the hydroxyl ion combine to form a molecule of water (H2O) ii. Hydrolysis o The reverse reaction of dehydration synthesis o “Water breaking apart” o breaks apart the molecule into its original subunits, with water donating a hydrogen ion to one subunit and a hydroxyl ion to the other iii. biological molecules fall into 4 general categories a. carbohydrates b. lipids c. proteins d. nucleotides/nucleic acids 3.3 WHAT ARE CARBOHYDRAT ES? Carbohydrates o Molecules are composed of carbon, hydrogen, and oxygen in the approximate ratio of 1:2:1 o All carbohydrates are a. Small b. Water-soluble sugars c. Polymers of sugars Monosaccharide o A carbohydrate consisting of just one sugar molecule o Also called “sugar” 3 Disaccharide o Two monosaccharides linked together o Also called “sugar” Polysaccharide o A polymer of many monosaccharides o Most do not dissolve in water at body temperature o Some serve as energy storage in molecules o Others strengthen the cell walls o Or form a supportive armor over bodies of insects, crabs, and their relatives A. There are Several Monosaccharides with slightly Different Structures i. Monosaccharides o Have a backbone of three to se ven carbon atoms o Most have both Hydrogen ( -H) and hydroxyl group ( -OH) attached to them ii. Sugar o When its dissolved in water it forms a ring usually o Common sugar is glucose iii. Glucose o Most common monosaccharide o Primary source of energy in cells iv. Many organisms s ynthesize other monosaccharides that have the same chemical formula s glucose but slightly different structures a. Fructose – plants b. Galactose – mammals v. Other monosaccharides o Ribose and deoxyribose § Have 5 carbons B. Disaccharides Consist of Two Monosaccharides Linked by Dehydration Synthesis i. Monosaccharides can be liked by dehydration synthesis to form disaccharides or polysaccharides ii. When energy required a. Disaccharides are broken apart by hydrolysis into their monosaccharide subunits b. Converted to glucose c. That is then broken down further to release energy stored in its chemical bonds C. Polysaccharides Are chains of monosaccharides 4 i. Starch o A polysaccharide o Plants use as an energy -storage molecule ii. Glycogen o Animals store this o Polymer of glucose molecules o Also a chain of glucose subunits, but more highly branched than starch iii. Cellulose o One of the most important structural polysaccharides o Makes up most of the walls of he living cells of plants o Makes up half the bulk of tree trunks iv. Chitin o Supportive outer coverings (exos keletons) of insects, crabs, and spiders o A polysaccharide in which the glucose subunits bear a nitrogen -containing functional group 3.4 WHAT ARE LIPIDS? Lipids o A diverse group of molecules that contain regions composed almost entirely of hydrogen and carbon o With non-polar carbon-carbon and cabon-hydrogen bonds o Some are used to store energy o Some form waterproof coverings o Some serve as the primary component of cellular membranes o Some are hormones o Three major groups a. Oils, fats, and waxes b. Phospholipids c. Steroids A. Oils, Fats, and Waxes a re Lipids Containing only Carbon, Hydrogen, and Oxygen i. Oils, fats, and waxes are built from only three types of atoms a. Carbon b. Hydrogen c. Oxygen o Each contain one or more fatty acid subunit ii. Fatty acid subunits 5 o Are long chains of carbon and hydrogen with a carbocyclic acid group ( - COOH) at one end iii. Fats and oils are formed by dehydration synthesis linking three fatty acid subunits to one molecule of *glycerol* • A three-carbon molecule iv. Triglycerides o Fats and oils chemical name v. Fats and oils o Used primarily as energy -storage molecules o Fats § are produced primarily by animals § the carbon of fatty acids are joined by single bonds, with hydrogen bonds at all other bonding sites o Oils are found primarily in the seeds of plants vi. Saturated o Fatty acids that contain as many hydrogen atoms as possible o Saturated fatty acid chains are straight and can pack closely together o Form a solid at room temperature vii. Unsaturated o Fatty acids with double bonds between some of the carbon atoms (fewer hydrogens) o Double bonds produce kinks in the fatty acid chains viii. Hydrogenation o Breaks some of the double bonds and adds hydrogens to the carbons o The process hydrogenation can convert liquid oils to solid ix. Waxes o Chemically similar to fats o Humans and most other mammals do not have th e appropriate enzymes to break them down o Highly saturated o Solid at normal outdoor temperatures B. Phospholipids Have Water -Soluble “Heads” and Water - Insoluble “Tails” i. Phospholipids o Plasma membrane that surround each cell contains several types of phospholipids o Similar to an oil, except one of the three fatty acids is replaced by a phosphate group attached to any of several polar functional groups that typically contain nitrogen 6 o Two dissimilar ends a. One end - two nonpolar fatty acid “tails” that are insoluble in water b. Other end – phosphate -nitrogen “head” that is polar and water soluble C. Steroids Contain Four Fused Carbon Rings i. Steroids o Composed of four rings of carbon atoms o All have similar, nonpolar, molecular structure with four fused carbon rings ii. Cholesterol o A steroid o A vital component of the membranes of animal cells o 2% of the human brain o used by cells to synthesize other steroids a. female sex hormone - estrogen b. male sec hormone – testosterone 3.5 WHAT ARE PROTEINS Proteins o Molecules composed of chains of amino acids o Estimated about 100,000 different types of proteins in human body Enzymes o Most cells contain hundreds of different enzymes o Proteins that promote specific chemical reactions Other Proteins o Keratin § Forms hair, horns, nails, scales, and feathers o Silk § Are secreted by silk moths and spiders to make cocoons and webs o Albumin § Found in egg white o Casein § Found in milk o Actin and Myosin § Contractile proteins that allow animal bodies to move A. Proteins are Formed from chains of Amino Acids i. Amino acids 7 o Proteins are polymers of amino acids o Joined by peptide bonds o All have the same fundamental structure a. Central carbon atom bonded to a hydrogen atom b. Nitrogen -containing amino group ( -NH2) c. Carbocyclic acid group ( -COOH) d. An “R” group that varies among differe nt amino acids ii. “R” group o gives each amino acid distinctive properties iii. Some amino acids are hydrophilic and water soluble because their “R” groups are polar iv. Others are hydrophobic, with nonpolar R groups that are insoluble in water v. The amino acid cysteine h as a sulfur-containing R group that can form covalent disulfide bonds o Disulfide bonds - play important roles in proteins C. Amino Acids Are joined by Dehydration Synthesis i. Proteins are formed by dehydration synthesis a. In proteins, the nitrogen in the amoino gr oup (-NH2) of one amino acid is joined to the carbon in the carboxylic acid group ( -COOH) of another amino acid by a single covalent bond b. Water is liberated ii. This bond is called a peptide bond iii. The resulting chain of two amino acids is called a peptide o A term used to relatively short chains of amino acids o Additionally, amino acids are added, one by one, until a polypeptide chain is complete iv. A protein consists of one or more polypeptide bonds D. A Protein can have as many as four levels of structure i. Interactions among amino acid R groups can cause twists, folds, and interconnections that give proteins their three dimensional structure ii. For organized levels of protein structure are possible: a. Primary b. Secondary c. Tertiary d. Quaternary iii. Primary structure o The sequence of amino acids in a protein 8 iv. The specific amino acids sequences cause polypeptides to assume simple, repeating secondary structures: a. A helix b. A pleated sheet o These are maintained by hydrogen bonds between the polar portions of amino acids v. Helix o The coiled, springlike secondary structure vi. Holding the turns of the coils together a. Hydrogen bonds that form between the oxygen atoms of the cardinal functional groups (with slightly negative charges) b. The hydrogens of the amino functional groups (with slightly p ositive charges) vii. Other proteins, such as silk o Contain polypeptide chains that repeatedly fullback upon themselves, with hydrogen bonds holding adjacent segments of the polypeptide together and a secondary pleated sheet arrangement. viii. Tertiary structures o Many proteins are contorted into these structures o They’re origami folds are determined by: a. the proteins the secondary structure b. its environment ix. quaternary structure o occurs in certain proteins that contain: a. individual polypeptides linked by hydrogen bonds b. disulfide bonds c. by attractions between oppositely charged portions of different amino acids o Each of the four polypeptides holds an iron containing organic molecule called a heme group, which can bind one molecule of oxygen E. The functions of proteins are related to their three-dimensional structures i. within a protein, the exact position in number of amino acids very specific R groups determined both: a. the structure of the protein b. its biological function ii. Denatured o a proteins normal three dimensional str ucture is altered while leaving the primary structure intact 9 o a denatured protein have different properties and will no longer performance its function 3.6 WHAT ARE NUCLEOTIDES AND NUCLEIC ACIDS Nucleotide o A molecule with a three part structure a. a five carbon sugar b. a phosphate functional group c. a nitrogen containing base Bases o I’ll have carbon and nitrogen items linked in rings, with functional groups attached to some of the carbon atoms Nucleotides o Fall into two general classes a. Deoxyribose nucleotides b. ribose nucleotides o this depends on which type of sugar they contain The bases in deoxyribose nucleotides: a. adenine b. guanine c. cytosine d. thymine The bases in ribose nucleotides a. adenine b. guanine c. cytosine d. uracil Nucleotide may function as: a. energy carrier molecules b. subunits of polymers called nucleic acids A. nucleotides act as energy carriers intracellular messengers i. Adenosine triphosphate (ATP) o A ribose nucleotide with three phosphate functional groups o ATP stores energy and bonds between its phosphate g roups o then releases energy when the bond linking the last phosphate to the ATP molecule is broken 10 o this energy is then available to drive energy demanding reactions such as linking amino acids to form proteins ii. the ribose nucleotide cyclic adenosine mono phosphate (cAMP) o ask as a messenger molecule himself iii. other nucleotides (NAD+ and FAD) are known as electron carriers because they transfer energy in the form of higher -energy electrons A. DNA and RNA, The Molecules of heredity, Are nucleic acids i. Nucleic acids o Single nucleotide (monomers) maybe strung together and long chains by dehydration synthesis, forming polymers called nucleic acids o an oxygen Adam in the phosphate functional group of one nucleotide is covalently bonded to the sugar of the next ii. deoxyribonucleic acid (DNA) o can contain millions of nucleotides o a DNA molecule consists of two strands of nucleotides entwined in the form of a double helix and linked by hydrogen bonds iii. ribonucleic acid (RNA) o Single stranded chains of ribose nucleotides o copied from the DNA o Direct the synthesis of proteins 11 Date CELL STRUCTURE AND F UNCTION 1. WHAT IS THE CELL TH EORY The Cell Theory • A fundamental concept of biology • Concluding that all cells come from previously existing cells • Consists of three principles a. every organism is made up of one or more cells b. the smallest organisms are single cells, and cells are the functional units of multi cellular organisms c. all cells arise from pre -existing cells 2. WHAT ARE THE BASIC A TTRIBUTES OF CELLS i. Cells perform and in Norma’s variety of functions a. Obtaining energy an d nutrients b. synthesizing biological molecules c. eliminating wastes d. interacting with other cells e. reproducing ii. diffusion o the process by which molecules dissolved in fluids dispersed from regions where their concentration is higher to regions where concentration is lower B. all cells share common features modern cells include the simple prokaryotic cells of bacteria and archaea, as well as far more complex eukaryotic cells of protists, fungi, plants, and animals C. the plasma membrane that encloses the cell and allows interactions between the cell and its environment i. plasma membrane o each cell is surrounded by an extremely thin, rather fluid membrane o important functions include: a. Selectively isolating the cells contents from the external environment b. Regulating the flow of materials into and out of the cell c. allowing communication with other cells in with the extracellular environment ii. phospholipid bilayer o helps isolate itself from its surroundings, allowing the cells to maintain essential differences and concentrations of material inside and outside D. all cells contain cytoplasm i. cytoplasm o consists of all the fluids and structures that lie inside the plasma membrane but outside of the nucleus ii. cytosol o the fluid portion of the cytoplasm in both prokary otic and eukaryotic cells o contains water, salt, and an assortment of organic molecules: a. proteins b. lipids c. carbohydrates d. sugars e. amino acids f. nucleotide E. all cells use DNA has a heredity blueprint and RNA to copy the blueprint and guide construction of cell parts i. deoxyribonucleic acid o the genetic material in cells o and inherited blueprint that stores instructions for making all the parts of the cell o for producing new cells ii. ribonucleic acid (RNA) o chemically similar to DNA o copies the genes on DNA o helps construct proteins based on this genetic blueprint F. there are two basic types of cells: prokaryotic and eukaryotic i. prokaryotic cells o form the bodies of bacteria and archaea, the simplest forms of life ii. Eukaryotic cells o Far more complex 2 o make up the bodies of animals, plants, fungi, and protists iii. organelles o the nucleus and other membrane enclosed structures o contribute to the far greater structural complexity of eukaryotic cells 3. WHAT ARE THE MAJOR F EATURES OF EUKARYOTI C CELLS? i. Eukaryotic cells o make up the bodies of animals, plants, protists, and fungi ii. the cytoplasm of all eukaryotic cells includes a variety of organelles B. some eukaryotic cells are supported by cell walls i. cell walls o the outer surface of plans, in some protists are covered wit h nonliving, relatively stiff coatings o secreted outside the plasma membrane o protect the delicate plasma membrane and it cytoplasmic contents C. the cytoskeleton provide shaped, support, and movement i. cytoskeleton o scaffolding of protein fibers within the c ytoplasm o three categories of cytoskeletal proteins: a. microfilaments ( composed of actin) b. intermediate filaments ( composed of various proteins) c. microtubules ( composed of tubulin) o important in regulating the following properties of cells: a. cell shape • in cells without cell walls, a scaffolding of intermediate filaments supports and determines the shape of the cell b. cell movement • Cell movement occurs as microfilaments on microtubules assemble, disassemble, or slide past one another c. Organelle movement • Microtubules transport organelles such as vesicles and mitochondria from place to place within a cell d. Cell division • microtubules dive chromosome movements, and microfilaments separate the dividing cell into two daughter cells D. Cilia and flagella new Vist a sell through fluid or move fluid past the cell 3 i. Cilia and flagella o Hair like structures that propel cells through fluids or move fluid past cells o Covered by extensions of the plasma membrane o supported internally by microtubules of the cytoskeleton ii. basal body o consists of a ring of nine fused triplets of microtubules located just beneath the plasma membrane iii. produce centrioles o produce basal body o identical and structure to basal bodies E. the nucleus, continuing DNA, is the control center of the eukaryo tic cell i. a cells DNA stores all the information needed to construct the cell and direct the countless chemical reactions necessary for life and reproduction ii. nucleus o large organelle with three major parts: a. nuclear envelope b. chromatin c. nucleolus iii. nuclear envelope o perforated by protein-lined nuclear pores § the nuclear pore complex lines each nuclear pore F. chromatin consists of strands of DNA associated with proteins i. chromosomes o made of DNA molecules and their associated proteins G. the nucleolus is the site of ribosome Assembly i. nucleolus o Eukaryotic nuclei contain at least one o The site of ribosome synthesis ii. ribosome o small particle composed of a type of RNA unique to ribosomes, called ribosomal RNA, combined with proteins. H. Eukaryotic cytoplasm contains membranes that form the endomembrane system i. endomembrane system o segregate molecules from the surrounding cytosol and ensure that biochemical processes occur in an orderly fashion ii. vesicles o small temporary socks made of membrane 4 iii. endoplasmic reticulum (ER) • series of interconnected membranes that form a labyrinth of flattened sacs and channels within the cytoplasm • Typically makes up at least 50% of the total membrane of the cell • Rough ER emerges from the ribosome covered outer nuclear membrane • smooth ER lacks ribosomes and is scarce in most cells iv. golgi apparatus o specialized set of membranes resembling a stack of flattened and interconnected sacs o performs the following functions: a. modify some molecules; and important role of the golgi is to add carbohydrates to proteins to make glycoproteins b. separates various proteins received from the ER according to their destinations c. packages the finished molecules into vesicles that are then transported to other parts of the cell or to the plasma membrane for export v. lysosomes o membrane-bound sacs that digest food ranging from individual proteins two microorganisms such as bacteria vi. food vacuole o the plasma membrane with its enclosed food pinches off inside the cytosol informs a vesicle called a foo d vacuole I. Vacuoles serve many functions, including water regulation, Storage, and support i. Contractile vacuoles o composed of collecting ducts, a central reservoir, And a tube leading to a pore v in the plasma membrane ii. Central vacuole o occupies three quarters or more of the volume of the most mature plant cells and serve several functions J. mitochondria extract Energy from food molecules and chloroplasts Capture solar energy i. endosymbiont hypothesis o holds that both mitochondria and chloroplasts evolved fr om prokaryotic bacteria ii. mitochondria o organelles that are sometimes called the “ Power houses” of the cell because they extract energy from food molecules and store it in high energy bonds of ATP. 5 iii. Chloroplasts o organelles surrounded by double membrane iv. chlorophyll o captures the energy of sunlight and transfers it to the other molecules in the thylakoid membranes during photosynthesis v. Plastids o organelles found only in plants in photosynthetic protists 4. WHAT ARE THE MAJOR F EATURES OF PROKARYOT IC CELLS? A. Prokaryotic self possessed specialized service features o nearly all prokaryotic cells are surrounded by a stiff cell wall o most are rock shaped bacilli o spiral shaped spirilla o or spherical cocci i. Pili o Surface proteins the project from the cell walls of many bacteria o two types: a. attachment pili - Short and abundant b. sex pili - few in number and quite long B. prokaryotic cells have fewer specialized cytoplasmic structures then do eukaryotic cells i. nucleoid o the cytoplasm of a typical prokaryotic cell conta ins a distinctive region called the nucleoid consisting primarily of DNA, with some RNA and protein ii. plasmids o located outside the nucleoid o Usually carry genes that give special prosperities 6 Date CELL MEMBRANE STRUCTURE AND FUNCTION 1. HOW IS THE STRUCTURE OF THE CELL MEMBRANE RELATED TO ITS FUNCTION ? Phospholipids • responsible for isolating the cell s contents Proteins • responsible for selectively exchanging substances and communic ating with the environment • controlling biochemical reactions associated with the cel l membrane • forming connections between cells Cell membrane functions: a. selectively isolate the contents of membrane enclosed organelles from the surrounding cytosol, and the cells conents fr om the surrounding interstitial fluid b. regulate the exchange of essential substances between the cell and the interstitial flui d, or between membrane enclosed organelles in the surrounding cytosol c. Allow communication among the cell of multi cellular organisms d. Create attachments within and between cells e. regulate many biochemical reactions B. membranes are “fluid mosaics” in which proteins move within layers of lipids i. Fluid mosaic model o Developed by Nicolson o now known to be accurate ii. fluid o any substance use molecules can flow past one another C. the fluid phospholipid bilayer helps to isolate the cells contents i. phospholipid o consists of two different parts : a. A “head” that is polar and hydrophili c b. A pair of fatty acid “tails” that are nonpolar and hydrophobic ii. interstitial fluid o a weekly salty liquid resembling blood without its cells or large proteins iii. Phospholipid by later o Phospholipids spontaneously arrange themselves into a double layer iv. cholesterol o all animal cell membranes contain cholesterol o especially abundant in the plasma membrane D. a variety of proteins form a mosaic within the me mbrane i. glycoproteins • some membrane proteins their carbohydrate groups that project from the outer membrane surface ii. membrane proteins maybe grouped into five major categories based on their function: a. enzymes b. receptor proteins c. recognition proteins d. connection proteins e. transport proteins iii. enzymes o proteins that promote chemical reactions that synthesize or break apart biological molecules iv. receptor proteins o dozens span cells plasma membrane o Allow cells to respond to specific messenge r molecules v. Recognition proteins o glycoproteins that serve as identification tags vi. connection proteins o anchors cell membranes in various ways vii. transport proteins o stanza phospholipid bilayer and regulate the movement of hydrophilic molecules across the membrane o some transport proteins from pores that can be opened or closed to allow specific substances to pa ss across the membrane 2. HOW DO SUBSTANCES MO VE ACROSS MEMBRANES ? 2 Membrane transport : a. solute § a substance that can be dissolve d in a solvent b. solvent § a fluid capable of dissolving the solute c. concentration § defines the amount of solute in a given amount of solvent d. gradient § a difference in certain properties , such as temperature , or the concentration of a solute in the fluid - between t wo adjacent regions e. concentration gradient § differences in solute concentration across their membranes B. Molecules and fluids defuse in response to gradients i. Diffusion o Random movements of solutes produce a net movement from regions of high concentration to regi ons of low concentration C. movement through membranes occurs buy passive transport and energy requiring transport i. selectively permeable o describes plasma membrane s o Their proteins selectively allow only certain ions or molecules to pass through, or permeate ii. Passive transport o involves diffusion of substances across cell membranes down their concentration gradient iii. Energy requiring transport o requires that the cell expend Energy to move substances across membranes D. passive transport include s simple diffusion, facilitated diffusion, and osmosis i. diffusion can occur within a fluid or cross a membra ne that is permeable to the diffusing substance ii. simple diffusion o some molecules diffuse directly through the phospholipid bilayer of cell membranes iii. facilitated diffusion o ions in polar molecules must you specific trans port proteins to move through so membranes 3 iv. Carrier proteins o span the cell membrane o have regions that loosely binds certain ions or specific molecules such as sugars or small proteins v. Channel proteins o form pores through the cell membrane vi. isotonic o Solutions with equal concentrations of solute ( and thus equal concentrations of water) are isotonic to one another vii. hypertonic o a solution that contains a greate r concentration of solute viii. hypotonic o a more dilute solution ix. turgor pressure o when water flows into the cytosol and then into the vacuole by osmosis o inflates the cell, forcing the cytosol within its surrounding plasma membrane against the cell wall E. Energy requiring transport includes acti ve transport, endocytosis, and exocytosis i. Active transport o membrane proteins use cellular energy to move molecules o r ions across the plasma membrane against their concentration grad ient o this means that the substances are transported from areas of lower concentration to areas of higher concentration o these proteins spend the width of the membrane and have two binding regions a. one loosely binds with the specific molecules or ion b. the second region, on the inside of the membrane, binds ATP ii. ATP o donates energy to the protein , causing the protein to change shape and move the calcium ion across the membrane o the energy for active transport comes from breaking the high -energy bond that links the last of the three phosphate groups in ATP iii. Endocytosis o a cell may need to acquire materials from its extra cellular environment that are too large to move directly through the membrane o this energy requiring process is endocytosis iv. pinocytosis 4 o very small patch of plasma membrane dimples inward as it surrounds interstitial fluid, and then the membrane bud s off into the cytosol as a tiny vesicle v. receptor mediated endocytosis o to specifically take up specific molecules or complexes of molecules that cannot move through channels or diffuse through the plasma membrane vi. Phagocytosis o
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