Principles of Biology I
Principles of Biology I BIOL 111
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Chapter13 MEIOSIS AND SEXUAL LIFE CYCLE Living organisms can reproduce their kind Inheritance or heredity is the transmission of traits from one generation to the next Variation is part of inheritance Genetics is the scientific study of heredity and genebased variation INHERITANCE OF GENES Genes are sections of DNA Genes contain a specific sequence of nucleotides Offspring acquire genes from parents by inheriting chromosomes Most genes program cells to synthesize specific enzymes and other proteins whose cumulative action produces an organism s inherited traits Gametes transmit genes from one generation to the next The DNA of eukaryotic cells is subdivided into chromosomes There tiny amounts of DNA in mitochondria and chloroplasts Each gene in an organism39s DNA has a specific locus plural loo on a certain chromosome COMPARISON OF ASEXUAL AND SEXUAL REPRODUCTION Asexual reproduction 0 One parent 0 Produces the offsprings by splitting budding orfragmenting o All the genes of the parent are passed on to the offspring o Offspring is genetically identical to the parent and is called a clone 0 No variation or little variation from parent and siblings due to mutations Sexual reproduction 0 Two parents 0 Union of two specialized cells known as gametes to form a single cell the zygote 0 Some of the genes of each parent are passed on to the offspring o The offspring is genetically diverse from each parent 0 Great variation from parents and siblings MEIOSIS The life cycle is the sequence of stages in the reproductive history of an organism from conception to the production of offspring THE HUMAN LIFE CYCLE o Somatic cells are cells other than a sperm or egg and have 46 chromosomes 0 Reproductive cells are known as gametes and have 23 chromosomes 0 The display of chromosomes is called the karyotype 0 Each chromosome found in somatic cells of higher plants and animals has a partner chromosome 0 The two partners of the pair are known as homologous chromosomes 0 The members of a homologous pair are commonly referred to as maternal and paternal chromosome because a different parent provided each 0 Homologous chromosomes carry similar but not identical genetic material that controls the same inherited character 0 Sex chromosomes are called X and Y and determine the sex of the individual All other chromosomes are called autosomes 0 Sex chromosomes are morphologically different from each other Females have XX chromosomes and males have XY chromosomes 0 Only a small part of the X chromosome is homologous with the small Y chromosome 0 Most of the X chromosome genes do not have a counterpart in the Y chromosome 0 Chromosomes formed by the separation of sister chromatids are however identical o If a cell contains two sets of chromosomes it is called diploid 2n If the cell has only one set of chromosomes then it is called haploid n 0 Sometimes cells may have more than one set of chromosomes and are called polyploid 3n 4n etc o The somatic cells of animals are diploid Only reproductive cells gametes are haploid o The process of meiosis produces haploid cells 0 Reduction in the number of chromosomes occurs before the formation of gametes o The fusion of gametes is called fertilization or syngamy o The resulting cell is called a zygote The zygote develops into a sexually mature individually All cells are derived from the zygote and receive the full complement of chromosomes during mitosis The only human cells not produced by mitosis are the gametes which are produced by meiosis Variety of sexual cycles The alternation of meiosis and fertilization is common to all organisms that reproduce sexually The timing of these events in the life cycle varies depending on the species A l Animals Fertilization 4 zygote 4 mitosis 4 diploid multicellular organism 4 meiosis 4 gametes 4 fertilization Most fungi and some algae Fertilization 4 zygote 4 meiosis 4 mitosis 4 haploid multicellular organism 4 gametes by mitosis 4 fertilization Plants and some algae Fertilization 4 zygote 4 mitosis 4 diploid multicellular organism sporophyte 4 meiosis 4 spores 4 mitosis 4 haploid multicellular organism gametophyte 4 mitosis 4 gametes 4 fertilization Alternation of generation sporophyte alternates with gametophyte THE PROCESS OF MEIOSIS Meiosis reduces the chromosome numberfrom diploid to haploid The phases of meiosis are similar to those of mitosis but with the following differences 1 Meiosis involves two successive nuclear and cytoplasmic divisions producing up to four cells l There are two consecutive cell divisions in meiosis meiosis and meiosis 3 DNA and other chromosomal components duplicate only once P Each cell produced by meiosis has only one set of chromosomes it is haploid 5 During meiosis the genetic information of both parents is shuffled so each resulting haploid cell has a unique combination of genes Meiosis Meiosis l separates homologous chromosomes not sister chromatids of individual chromosomes During the interphase Chromosomes replicate during the 8 stage of the interphase Each chromosome consists of two genetically identical sister chromatids connected at the centromere The centrosome replicates forming two centrosomes 1 Prophase l the nuclear envelope disintegrates chromosomes condense the chromosome members of a pair become to lie lengthwise side by side in what is called synapsis l The four chromatids lying side by side are called tetrads a term preferred by geneticists The term tetrad refers to the four chromatids two forming each homologous chromosomes Bivalent is another term synonym of tetrad and preferred by cytologists During synapsis the chromosomes undergo crossing over The place where the chromosomes cross is called chiasma plural chiasmata Crossingover is a process of genetic recombination in which homologous chromosomes exchange sections of DNA chromatids break exchange sections of DNA and rejoin There is no crossingover between sister chromatids The synaptonemal complex made of proteins is formed between synapsed homologous chromosomes and holds the chromosomes together Centrosomes move away from each other and the spindle of microtubules forms between them The nuclear envelope disintegrates The microtubules of the spindle attach to the kinetochores and the chromosomes begin to move to the metaphase position Metaphase l tetrads line up in the equatorial plane forming the metaphase plate and are held together by chiasmata sing chiasma In late prophase l homologous chromosomes are held together only at chiasmata the regions where crossing over occurred o Microtubules from one pole are attached to one homologous chromosome and those from the other pole to the other homologous chromosome 0 Both kinetochores of sister chromatids are attached to the same pole o In mitosis sister kinetochores are attached to opposite pole 3 Anaphase I the members of each homologous pair separate and move to opposite poles 0 Each pole receives a mixture of maternal and paternal chromosomes but only one member of the homologous pair 0 The sister chromatids are still united at their centromere region 4 Telophase l nuclear envelope may a 39 39 39 39 39 cytokinesis may take place 0 Homologous chromosomes continue to move apart until the reach the poles of the cell Each pole has now a haploid number of chromosomes 0 Each nucleus contains only a haploid number of chromosomes 0 Each chromosome however has two sister chromatids 5 Cytokinesis usually occurs simultaneously with telophase o Cleavage furrows form in animal cells and cell plate appears in plant cells 0 In some species nucleoli reforms and chromosomes decondense This interlude is called interkinesis o No chromosome replication occurs between the end of meiosis l and the beginning of meiosis ll Meiosis ll Meiosis II is similar to mitosis and results in the separation of the sister chromatids Prophase Spindle apparatus forms and centrosomes move toward the poles Metaphase o Chromosomes form the metaphase plate 0 The kinetochores of each sister chromatid point toward opposite poles Anaphase II o The centromeres of the sister chromatids separate and the sister chromatids become separate chromosomes 0 Chromosomes move toward opposite poles Telophase II and cytokinesis o A nuclear envelope reforms around each set of chromosomes nucleoli are also formed spindle disappears chromosomes uncoil o Cleavage furrows form in animal cells and cell plate appears in plant cells COMPARISON OF MITOSIS AND MEIOSIS 1 Synapsis and crossing over occur only in meiosis never in mitosis 2 Homologous chromosomes paired up at the metaphase plate I during meiosis in mitosis the chromosomes are not paired during at the metaphase plate 3 During anaphase I of meiosis each homologous chromosome moves to an opposite pole but the sister chromatids remain attached by the centromere in mitosis the sister chromatids separate during the anaphase GENETIC VARIATION Sexual life cycles are responsible for most of the variation that is found in each generation There are three mechanisms that reshuffle the genes carried by individuals Independent assortment of chromosomes In metaphase I the homologous pairs of chromosomes consist of one maternal and one paternal chromosome The positioning of each homologous chromosome pair during metaphase is a matter of chance and independent of the other pairs This determines which chromosomes will be together in the daughter cells Each homologous pair is positioned independently of other pairs There is a 5050 chance that a daughter cell will get a maternal or a paternal chromosome of a given homologous pair The number of daughter cells formed by meiosis of diploid cells is 4 2n 4 In the case of humans the haploid number of chromosomes is 23 and the number of possible combinations of maternal and paternal chromosomes in the resulting gametes is 223 or roughly 83 million Crossing over During prophase l homologous chromosomes pair precisely aligning with each other gene by gene Nonsister chromatids of homologous chromosomes exchange segments of DNA This process gives rise to recombinant DNA e g a segment of the paternal chromosome is exchange from a similar segment of the maternal chromosome Random fertilization Due to the large number of possible combinations in human gametes the number of possibilities is in the trillions The fusion of a male and a female human gamete will produce one of a possible 70 trillion combinations 223 x 223 70 trillions To this add the variation brought about by crossing over This is why brothers and sisters are different Evolutionary adaptation Darwin recognized the importance of genetic variation in the mechanism of natural selection Evolutionary adaptation depends on the genetic variation found in the population On the average those individuals best suited to the local environment survive leave the greatest number of offspring and transmit their genes in the process This selection of bestsuited individuals results in an accumulation over time of the genetic variations favored by the environment Chapter15 THE CHROMOSOMAL BASIS OF INHERITANCE Mendel39s work remained buried in libraries until 1900 when it was discovered independently by three scientists working on plantbreeding experiments 0 German Karl Correns Austrian Erich von Tschermak Dutchman Hugo de Vries 0 Their results agreed with those of Mendel o Mendel39s paper provided the explanation for their results Many biologists remained incredulous of Mendel39s Law of segregation and independent assortment until evidence showed that there was a physical basis for these principles in the behavior of the chromosomes In 1902 Walter Sutton Therodor Boveri and others independently noted the parallels between the behavior of the chromosomes and the behavior of Mendel39s factors 0 Chromosome Theory of Inheritance 0 Genes have specific loci on chromosomes and it is the chromosomes that undergo segregation and independent assortment Thomas Hunt Morgan traced a gene to a location in a sex chromosome 0 Eyecolor gene in fruit flies is found in the X sex chromosome Genes located in the sex chromosomes are called sexlinked genes Each chromosome has hundreds of thousands of genes Each chromosome has a linear arrangement of specific gene loci LINKAGE Linked genes tend to be inherited together because they are located near each other on the same chromosome Linked genes do not assort independently During the anaphase all these genes in the same chromosome move together to the pole Independent assortment of chromosomes and crossing over produce genetic recombinants When offspring show the same phenotype as the parents they are called parental types When offspring have new combination of characters they are called recombinants o In nonlinked genes 50 of the offspring are recombinants Recombination between linked genes occurs due to crossing over A recombination frequency of less than 50 indicates that genes are linked but that crossing over has occurred Exchange of genetic material between homologous chromosomes breaks linkages and establishes new linkages During prophase of meiosis l paired homologous chromosomes break and corresponding points and switch fragments creating new combinations of alleles that are then passed on to the gametes Some genes in long chromosomes are so far from each other that cross over between them is almost certain These genes have a frequency over 50 and virtually the same as genes in different chromosomes GENETIC MAPS A ordered list of genetic loci along a particular chromosome is called a genetic map Sturtevant develop a system of finding the relative position of genes along the chromosome using recombination frequencies Genetic maps based on recombination frequencies are called linkage maps 1 map unit is equivalent to a 1 recombination frequency now it is called a centimorgan Geneticists use recombination data to map a chromosome39s genetic loci The farther apart genes are in a chromosome the more likely they are to be separated during crossing over lfthe genes are at the extremes of the chromosome crossing over is almost a certainty and cannot be distinguished in genetic crossing from nonlinked genes Theirfrequency is 50 Linkage maps give the sequence of genes along the chromosome but do not give the specific location of each gene Cytological maps are based on detectable chromosome abnormalities or markings seen in the microscope SEX CHROMOSOMES Sex is commonly determined by special sex chromosomes Typically one sex is homogametic that is it has a pair of similar chromosomes The other sex is heterogametic It has two different sex chromosomes chromosomes In many animals the female is homogametic XX and the male heterogametic XY 0 In some insects eg grasshoppers roaches XX if female and X male 0 ln birds some fishes and some insects ZW is female and 22 male 0 In most bees and ants no sex chromosomes diploid animals are females haploid are males males have no fathers they develop from unfertilized eggs Chromosomes other than the sex chromosomes are called autosomes The Y chromosome determines male sex in many mammals The X chromosomes has many important genes unrelated to sex determination and needed in both males and females Genes found in the X chromosome are called sexlinked genes Y chromosome has several genes involved in determining the male sex Sex linked genes have a unique pattern of inheritance Some individuals have an abnormal number of sex chromosomes The anatomical features of gender begin to appear in the embryo at about 2 month of age Prior to that age the gonads are generic and could develop into either sex according to the prevalent hormones in the embryo The SRY gene in the Y chromosome triggers the development of testis There are other genes involved in the development of a normal male In the absence of the SRY gene the gonads develop into ovaries Xlinked genes have an unusual pattern of inheritance Males are neither homozygous nor heterozygous for Xlinked genes They are called hemizygous See facts about the Y chromosome on Sexlinked disorders are more common in males than in females because the female has to have both recessive genes to show the phenotype while the male will show whatever allele is in the X chromosome whether dominant or recessive o Hemophilia color blindness and Duchenne muscular dystrophy are sexlinked genes Dosage competition is a mechanism that makes the two doses of in female and the single dose in the male equivalent In mammals dosage competition is accomplished by the inactivation of one X chromosome The metabolically inactive X chromosomes is called a Barr body Inactivation of the X chromosome occurs randomly in each cell of the body resulting in variegation The Barr body has one active gene the XIST gene This gene produces multiple copies of an RNA that covers the entire chromosome The inactivation occurs when an methyl group CH3 is attached to the base cytosine of the DNA nucleotides The process is not well understood Sexinfluenced genes are autosomal genes whose expression is affected by the individual sex Some individuals have an abnormal number of sex chromosomes 0 XXY Klinefelter syndrome is male with underdeveloped testes but otherwise almost normal male appearance 0 X0 Turner syndrome has the appearance of an immature female 0 YO embryos do not survive ERRORS AND EXCEPTIONS IN CHROMOSOMAL INHERITANCE Karyotype refers to the number of chromosomes of an individual and to the photomicrograph showing the chromosomes Nondisjunction occurs when homologous chromosomes fail to segregate during meiosis Aneuploidy is the presence or absence of a single extra chromosome It is more common in humans than polyploidy o Trisomic individuals have three chromosomes of a kind 0 Monosomic individuals have a single chromosome of a kind 0 Aneuploidy is due to abnormal mitosis or meiosis when the chromosomes fail to separate in the anaphase This is called nondisjunction Polyploidy is the presence of several chromosome sets It is common in plants but rare in animals 0 Polyploidy is lethal in humans if it occurs in all cells of the body 0 A few triploid and tetraploid individuals have been born alive and survived a few days They were found to have a mixture of diploid and polyploid cells Alterations in chromosome structure Breakage of chromosomes can lead to four types of alterations in chromosomal structure V V Deletions are loss of chromosomal material A chromosome breaks and fails to rejoin Most deletions are lethal Criduchat is due to a deletion in chromosome 5 Duplication occurs when a piece of a chromosome breaks off and becomes attached on the sister chromatid causing a duplication of genetic material in the recipient chromosome An inversion happens when the detached piece is reattached to its chromosome but in the reverse orientation Translocation is the attachment of part of a chromosome to a nonhomologous chromosome Nonhomologous chromosomes may a parts 39F It may result in the elimination or duplication of genes A type of Down syndrome results from the translocation of a portion of chromosome 21 to chromosome 14 The individual has two normal chromosomes 21 one normal chromosome 14 and one abnormal chromosome 14 with a portion of chromosome 21 attached In chronic myelogenous leukemia CML a piece of chromosome 22 has switched places with a fragment from the tip of chromosome 9 The production of white blood cells is affected Deletions and duplication are especially likely to occur during meiosis Duplication and translocation tend to have harmful effects because essential genes may be affected lnversions do not cause an imbalance in the genes but the change in location may influence the phenotype due its new location and neighboring genes Certain cancers are I I L39 due to HUMAN DISORDERS DUE TO CHROMOSOMAL ALTERATIONS Down syndrome or trisomy 21 is the most common trisomy in humans Kleinfelter syndrome XXY is a male with underdeveloped testes enlarged breasts and one Barr body per cell Females with XXX trisomy are normal and cannot be distinguished from XX females except by studying the karyotype It occurs about 1 in a 1000 births Turner syndrome X0 is an example of monosomy The individual is a female with degenerate ovaries slight mental retardation in some and webbed neck o Autosomal monosomy has not been seeing in live births It probably results in the death of the embryo at a very early stage 0 17 20 of all pregnancies recognized at 8 weeks result in spontaneous abortion miscarriage About have of these embryos have chromosome abnormalities Autosomal monosomy is very rare in embryos this old PHENOTYPIC EFFECTS The phenotypic effect of some mammalian genes depends on whether they were inherited from the mother of from the father Most imprinted genes are on autosomes they are not sexlinked Genomic imprinting Imprinting occurs during the formation of gametes and results in the silencing of one allele of certain genes These genes are imprinted differently in sperm and ova The zygote expresses only one allele of an imprinted gene either the allele inherited from the male parent or the female parent The imprints are transmitted to all the body cells during development When gametes are produced in the new generation imprints are erased in gamete producing cells and the chromosomes of the developing gametes are newly imprinted according to the sex of the individual 0 A gene imprinted for maternal allele expression is always to be imprinted for maternal allele expression and not for paternal allele expression It seems that the heavy methylation of cytosine nucleotides of one of the alleles inactivates the gene However for some genes methylation activates its expression Imprinting affects only a small fraction of the genes but most of the known imprinted genes are critical for embryonic development Normal development apparently requires that embryonic ells have exactly one active copy not zero not two of certain genes Extranuclear genes Mitochondria and chloroplasts have their own genes The sperm does not contribute any cytoplasm to the zygote Because the zygote39s cytoplasm comes from the ovum some phenotypic features of the offspring depend only on the maternal cytoplasmic genes e g mitochondrial genes Some diseases of the muscular and nervous systems depend on defective mitochondrial genes that prevent cells from making enough ATP Defective mitochondrial DNA may be involved in some cases of heart diseases diabetes and Alzheimer39s disease The variegated leaves of plants depend on plastids which are contributed by the mother plant only The pollen grain does not contribute any cytoplasm to the plant zygote Extracellular genes do not follow the Mendelian rules of inheritance Chapter 28 There are fossil remains that seem to indicate that eukaryotes appeared on earth as early as 27 billion years ago Kingdom Protista is an artificial grouping AND many biologists have abandoned it Classification does not represent evolutionary relationships Systematists have split protists into as many as 20 kingdoms There are about 60000 species of protists PROTISTS ARE A VERY DIVERSE GROUP Protists are Eukaryotes have true nucleus membrane bound organelles 92 flagella and cilia Most are small singlecelled organisms some are coenocytic multinucleated colonial and some are multicellular Almost all are aerobic using mitochondria for cellular respiration Anaerobic forms live in anaerobic environment and lack mitochondria or have mutualistic respiring bacteria Some have chloroplasts and manufacture their own food like plants Photosynthesizers Algae Others ingest food like animals Heterotrophs Protozoa Others absorb food like fungi Absorbers Funguslike protists Mixotrophs combine photosynthesis and heterotrophic nutrition Interesting websites httphinlnnv unm 39 ilBioloqy 203 quot 39 quotquottists htm httpwww 39 39 39 39 39 quot quot quot 39 Wnnn htm httpwww sidwell 39 39 vlb5LabsP39 quot39 quot ahFukarvaProtista httpWWW 39 quot quot quot 39 39 39 39 01htm ORIGIN AND DIVERSIFICATION OF EUKARYOTES In some groups of prokaryotes increasing complexity evolved by 0 Becoming multicellularfilamentous where different cell types perform different functions e g some cyanobacteria o The evolution of complex communities e g stromatolites o The development of compartmentalization within the cell that produced eukaryotes Endosymbiont hypothesis proposed by Merschkovsky and developed by Margulis and others An endosymbiont is a cell that lives inside other cells or tissues Eukaryotic cells evolved from prokaryotic cells that incorporated other prokaryotic cells using the mechanism of endocytosis Mitochondria and chloroplasts were originally small prokaryotes living within larger cells 0 Chloroplasts developed from photosynthetic cyanobacteria o Mitochondria were formed from aerobic heterotrophic bacteria 0 Flagella cilia centrioles and other structures are made of microtubules and appear to be homologous They arose by the capture of spirochetelike prokaryotes the evidence of this is not strong Secondary endosym biosis Some algal groups have plastid envelopes with three or four membranes Euglena has a threemembrane envelope and belongs to a group of protists that also includes flagellated heterotrophic forms lacking plastids A hypothesis states that plastids were acquired independently several times during the early evolution of eukaryotes Each evolutionary event added one more membrane derived from the vacuole membrane of the host cell that engulfed the endosymbiont In some cases of secondary endosymbiosis the endosymbiont lost all its parts except the plastid In other cases remnants of other parts are still present Interesting websites httpusersrcncom39kimballmaultranetBioloqua quotquot 39 quot 39 html httpwwwmrsumnedugoochvCellBiolecturesendoendohtml PROTISTAN DIVERSITY Many biologists have abandoned the Kingdom Protista Others keep it for convenience until phylogenetic problems are resolved A new hypothesis recognizes five supergroups of eukaryotes l EXCAVATA The excavata is a recently proposed group that is based on morphological studies of the cytoskeleton Some members have an excavate feeding grove on one side of the cell body DIPLOMONADS 0 Two haploid nuclei 0 Have multiple flagella o Modified mitochondria called mitosomes 0 They get their energy through fermentation 0 They have a very simple cytoskeleton o Heterotrophs most are commensals in the intestine of animals some are free living and others are parasitic Interesting sites ht39tn39lhinlnm kenvnn I Iquot II I I I I I 1 Iquot I I I II I quotI htmldes E httpWWWquot 39 39 quot quot39 39 Giardia lamblia PARABASALIDS 391 I Have reduced called 39 39 they generate some energy anaerobically releasing hydrogen gas as a biproduct Heterotrophs either commensals in the digestive track of insects or parasitic in animals Apparently capable of digesting cellulose Undulating membrane along the length of the cell EUGLENOZOA This is a diverse clade that includes predatory39 39 and parasites They all have a spiral crystalline rod of unknown function inside their flagella KINETOPLASTIDA o A single large mitochondrion associated with a unique organelle the kinetoplast which is single mass of extranuclear DNA 0 They are flagellated and therefore motile some are colonial 0 Sexual reproduction has not been observed 0 Heterotrophs free living consumers of prokaryotes parasites of plants and animals e g Trypanosoma causes the African sleeping sickness Chagas disease EUGLENOIDS o Euglenoids have two flagella one short and one long 0 They have chlorophyll a and b carotenoids and xanthophylls 0 They possess flexible internal protein plates but lack cell wall 0 They are heterotrophic in the absence of light CHROMALVEOLATA This supergroup is an extremely diverse clade It has been recently proposed based on two lines of evidence 1 DNA sequence data suggest that they form a monophyletic group 2 Some data support the hypothesis that they originated more than a billion years ago when a common ancestor of the group engulfed a singlecelled photosynthetic red alga ALVEOLATA The alveolates have small membrane bounded cavities undertheir cell surfaces The function of the cavities or alveoli is uncertain There are three groups in the alveolata 1 Dinoflagellates aquatic autotrophs 2 Apicomplexans parasitic organisms that produce sporozoites 3 Ciliates heterotrophs that move by cilia Interesting websites httpwwwurmn herkelpv 39 39 39 I I I 1 mm DINOFLAGELLATES They are a major component of phytoplankton and the basis for marine food chains Most are unicellular and some are colonial They have two flagella Many are covered with cellulose plates They have chlorophyll a and c carotenoids and fucoxanthin a yellowbrown carotenoid Many are mixotrophic and about half are purely heterotrophic Some produce bioluminescence some produce neurotoxins They have a characteristic type of nuclear and cell division Their chromosomes are always condensed See special mitosis page 237 Reproduction is mostly asexual but sexual reproduction has been observed in some species httpwwwurmnherkelpv quotF 39 II39 n u 1 hfml httphinlnm kenvnn 39 39 39 n I 1 hfml APICOMPLEXANS Parasitic protozoan that lack structures for locomotion Their infectious cells are called sporozoites nonresistant compact infective cells Complex of apex organelles fibrils microtubules vacuoles etc specialized to penetrate host cells and tissues 0 Apicoplast an organelle involved in the synthesis of fatty acids They move by flexing They have a complex life cycle with sexual and asexual reproduction involved They require two or more species to complete their life cycle eg the malaria Plasmodium CILIATES 0 Members of this group are unicellular and use cilia for locomotion 0 They are covered with the pellicle which gives them a definite but flexible shape 0 Solitary and motile or colonial and sessile 0 They have two types of nuclei a macronucleus that controls metabolism and one or several micronuclei that function in the sexual process Generally reproduce asexually by binary fission in which the macronucleus disintegrates and a new one is formed from the cell s micronuclei Sexual reproduction by conjugation httphome1gtenetvs39slsk1stalkedciliateshtm httpwwwsotonacukcebDiagnosisNol2htm STRAMENOPILA The stramenopiles have been grouped on the basis of similarities of the ribosomal RNA gene sequence They have a quothairyquot flagellum and nonhairy one In most groups the only flagellated stages are the motile reproductive cells Some of these groups are commonly called algae DIATOMS Mostly unicellular with some colonial forms covered with a shell of silica silicon dioxide embedded in an organic matrix They are nonmotile but some forms glide over a secreted slime Their plastids contain chlorophyll a and c carotenoids and xanthophylls Energy reserves are stored as oils and a carbohydrate called chrysolaminarin Reproduction is usually asexual sexual stages are rare Diatomaceous earths are made of fossil diatoms CHRYSOPHYTES OR GOLDEN ALGAE They are unicellular and colonial organisms bearing two flagella on the anterior end Their plastids contain chlorophyll a and c carotenoids and xanthophylls Energy reserves are stored as oils and the carbohydrate laminarin Some species are mixotrophic they can turn to predation in the absence of light or absorb dissolved organic compounds Cells are covered with tiny scales made of silica or calcium carbonate o Reproduction is primarily asexual involving the production of motile spores called zoospores httpwww urmn herkelev 1 1 anntha html BROWN ALGAE OR PHAEOPHYTA All are multicellular organisms the largest and more complex of protists may have blades stipes and holdfast these structure forms the thallus or body Kelps may reach more than 30 feet in length They have chlorophyll a and c and fucoxanthin Store carbohydrate in the form of laminarin Their cell wall is made of cellulose and algin There are several types of life cycles with alternation of generation The generations may be isomorphic or heteromorphic Seaweeds have structural and biochemical adaptations that allow them to survive and reproduce in a harsh habitat Seaweed is a general term that includes the brown red and green algae They have a holdfast for attachment a stemlike stipe and the leaflike blades The body of the seaweed is called the thallus They normally inhabit the intertidal and subtidal zones near the shoreline Their cell wall has cellulose and a gelforming polysaccharide that helps cushion the thallus against the agitation of the waves Brown algae produce algin red algae produce agar and carageenan Alternation of generation is a complex life cycle in which the multicellular diploid sporophyte alternates with a multicellular haploid gametophyte If the sporophyte and gametophyte are similar in appearance they are called isomorphic if different they are called heteromorphic httpwwwurmn herkelev 39 39 39 1 I I I 4 hfml OOMYCETES OR WATER MOLDS They have a filamentous body called a mycelium Each filament is called a hypha Mycelium is coenocytic They grow over organic matter digesting it and absorbing it The cell walls are made of cellulose They reproduce asexually by forming motile zoospores or sexually by fusion of gametes Biflagellated zoospores have two kinds of flagella one hairy and one smooth The sexually produced zygote is thickwalled and it is called an oospore The diploid condition dominates the life cycle 0 Some are important plant pathogens They include water molds white rusts and downy mildew httpwwwurmn herkelpv 39 39 39 1 I L hfml httphntit hntanv wisr 39 quot quotNOF amp I httpWWW mvmlnn 39 39 1 hfm IV RHIZARIANS This group has been recently proposed based on DNA similarities which suggest that the group is monophyletic Rhizarians are distinguished from amoebas by having threadlike pseudopodia FORAMINIFERANS Phylum Foraminifera These are marine and freshwater unicellular organisms that produce shells or tests made of calcium carbonate They form cytoplasmic projections pseudopodia through small openings in the test that function is swimming feeding and shell formation httpwwwucmpberkeleyeduforamforamintrohtml httpuserwwwsfsuedubiol240labslab f quot quot 39 html RADIOLARIANS OR ACTINOPODS Phylum Actinopoda a polyphyletic group grouped for convenience They are heterotrophic unicellular and mostly planktonic organisms found in fresh and saltwater Actinopods have cytoplasmic p j quot called microtubules thinly covered with cytoplasm Axopods delay sinking and help in the capture of prey and particles Many are covered with mineral skeletons of silica and sometimes containing organic substances 0 Many contain algal endosymbionts I39 39 with bundles of httpwww nersnnal nsu 39 quotquot quot39 7W 39 quot html httpwww ur mn herkelev 39 quot 39 im mrlmm html V OTHER ALGAE The red algae green algae and land plants make the fourth supergroup RED ALGAE Phylum Rhodophyta They are mostly multicellular but some are unicellular They live primarily in warm marine habitats but some are found in fresh water and soil They have chlorophyll a and some quot 39 quot d quot pl 39 and phycoerythrin The accessory pigments phycocyanin and phycoerythrin are adaptation to living in deep water they absorb blue and green light that penetrates more deeply into the water Some species lack pigment and live as parasites of other red algae Nuclear envelope does not disintegrate during mitosis See page 237 Red algae never form motile gametes Store their energy reserve as floridean starch similar to glycogen Cell wall is made of cellulose agar and carrageen All red algae reproduce sexually and have no flagellated stages Alternation of generations is common and some have a complex life cycle httpiIwwwurmnherkelpv quotF 39 II I I4 hfml httptolweborgtreegroupRhodophyta httpwww life umd 39 labsdelwichePSlifelecturesRhodo h tahtml GREEN ALGAE OR CHLOROPHYTA o Phylum Chlorophyta 0 Mostly fresh water inhabitants but also found in saltwater and moist land places 0 Green algae have a variety of body types unicellular colonial filamentous and wide leaflike body 0 Their pigments energy reserve products and cell wall are chemically identical to those of plants 0 They have chlorophyll a and b carotenoids and the energy reserve is starch 0 Their chloroplasts are similar to those of plants 0 Most have complex life history involving sexual and asexual stages Some show alternation of generations 0 Their gametes are biflagellated with a varied morphology isogamy anisogamy and oogamy o Spirogyra reproduces sexually by conjugation an exception within the Chlorophyta o Probably within this group is the ancestor of land plants Larger size and greater complexity evolved in chlorophytes by three different mechanisms 1 Formation of colonies and filaments 2 Formation of true multicellular bodies b cell division and differentiation 3 Repeated division of the nuclei with no cytokinesis httpwww urmn hprkplpv 39 39 I I hfml httn39lhvnnea hntanv uwr ar 39 39 39 39 39H I I Ihtm u I hm I 39 39 quot htMzi1XJampsdnsaltaduariumampzuhttp3A 2F2Fvisnr nlanthin nhinu edu239 39 39 I I I 4 mm VI UNIKONTS This group includes animals fungi and some protists There are two major groups of unikonts amoebozoans and opisthokonts These two major groups are strongly supported by molecular systematics AMOEBOZOANS Amoebozoans move and feed by means of pseudopodia cellular extensions capable of changing shape elongating and contracting They feed on bacteria protists and detritus PLASMODIAL SLIME MOLDS The plasmoclium is a multinucleated gigantic cell up to 1 foot in diameter lt creeps along the forest floor ingesting bacteria and other pieces of organic matter It often forms a network of channels When stressed it ceases to grow and form sexually reproductive structures called sporangia in which spores are produced through meiosis The spores will germinate and produce a biflagellated cell called a swarm cell or an amoeboid cell called a myxamoeba Both types act as gametes o A zygote is formed by the fusion of gametes The resulting diploid nucleus divides many times by mitosis forming a new multinucleated plasmodium CELLULAR SLIME MOLDS Phylum Dictyostelida o The feeding stage consists of solitary haploid cells 0 When the food supply is depleted the cells aggregate to form a mass called pseudoplasmodium or slug 0 The cells remain separate and maintain their own identity the nuclei are haploid o The slug produces a stalked fruiting body that produces haploid spores o The haploid spores produce more haploid solitary cells 0 Sexual reproduction has been observed on occasion by the fusion of haploid cells 0 No flagellated stage present Slime molds were thought to be fungi because the produce spores in structures similar to those found fungi These protists differ from true fungi in having centrioles and cell wall made of cellulose Molecular systematics places them in the Amoebozoa and may be descendants of gymnamoebalike ancestors Other slime mold sites httpwwwucmpberkeleyeduprotistaslimemoldshtml httpwwwinfopleasecomce6sciA0845543html httpwwwcscucedutfutcherSlimemoldshtml GYMNAMOEBAS 0 They are freeliving shapeless and unicellular with a flexible body they lack shell 0 Move by means of pseudopodia 0 Some species are multinucleated 0 Feed by endocytosis httpWWW 39 quot39I am 39 quot 39 htmlht39tn39www uk nrn 39 11amnnhg hfml httpnowifmoruameco ENTAMOEBAS o Entamoebas are unicellular and parasitic they infect vertebrates and invertebrates 0 They cause dysentery httphomepageslshtmacukentamoeba httpwwwcdfoundtoitHTMLenta3htm httpWWW innvista quot 39 39 39 ECOLOGICAL RELATIONSHIPS Symbiotic protists form a wide range of mutualistic and parasitic relationships that affect their partners and many members of their community Photosynthetic protists are among the most important producers in aquatic ecosystems They are at the base of the food web SUMMARY Diplomonadida two equalsized nuclei lack mitochondria have multiple flagella Parabasala anaerobe eukaryotes lack mitochondria amoebalike cell some flagellated Euglenozoa photosynthetic and heterotrophic flagellates 1 Euglenoids two flagella paramylon 2 Kinetoplastida A single large mitochondrion associated with an unique organelle the kinetoplast which contains extranuclear DNA Alveolata unicellular protists with subsurface cavities 1 Dinoflagellates two flagella many are covered with cellulose plates 2 Apicomplexans lack structures for locomotion parasitic complex life cycle 3 Ciliates cilia two types of nuclei Stramenopila water molds and heterokont algae quothairyquot flagellum and nonhairy one 1 Water molds or oomycota filamentous body hyphae zoospores 2 Diatoms shell a box of silica nonmotile or gliding movement 3 Golden algae carbohydrate laminarin two flagella 4 Brown algae large multicellular cell wall is made of cellulose and algin Foraminiferans tests or shells of CaC03 cytoplasmic projections through small openings in the test that function is swimming feeding and shell formation Radiolarians or Actinopods cytoplasmic j quot called quot 39 39 with bundles of microtubules thinly covered with cytoplasm Unikonts Amoebozoan shapeless and unicellular pseudopodia feed by endocytosis 1 Gymnamoebas free living in soil and water 2 Entamoebas parasites of animals 3 Plasmodial slime molds unicellular multinucleated gigantic cell called plasmodium fruiting bodies produce spores 4 Cellular slime molds unicellular haploid stage cells aggregate to form a mass called pseudoplasmodium or slug fruiting bodies Rhodophyta lack flagellated cells phycoerythrin cell wall of cellulose agar and carageenan Chlorophyta plantlike chloroplasts chlorophyll a and b starch biflagellated gametes httpwwwsidwelleduussciencevlb6labsquot quot39 quot l ahFllkarvaProtista httpwww snea indiana 39 quot quotelfl5I5chrvsophvtahtm httpwww 39 39 nrn quot hrmlhttpWWW uk nrn 39 11amnnhg hfml Chapter16 THE MOLECULAR BASIS OF INHERITANCE GENES CARRY INFORMATION Early geneticists thought that genes were made of proteins Archibald Garrod 1908 introduced the idea that genes and enzymes are related 0 Discussed the genetic disease alkaptoneuria o Homogentisic acid HA an intermediate of the breakdown of phenylalanine and tyrosine is excreted in the urine 0 Garrod theorized that an enzyme that oxidizes HA was lacking and that this was due to a mutation of the gene James Sumner 1926 showed that enzymes were proteins Frederick Griffith 1928 converted avirulent pneumococcus to the virulent strain 0 Experiment with mice injected with avirulent live cells and heatkilled virulent cells 0 Avirulent cells were converted to virulent cells 0 Transformation due to a transforming principle OT Avery CM McLeod and M McCarty 1944 identified the transforming principle to be DNA George Beadle and Edward Tatum 1940s suggested that a single gene specifies each protein 0 They worked with fungus Neurospora crassa o Neurospora is a haploid organism 0 One gene one protein hypothesis Alfred Hersheyand MarthaChase 1952 39 39 I 39 onthe 39 quot of bacteriophages 0 They showed that DNA enters the cell 0 DNA is required for synthesis of new protein coats and DNA Erwin Chargaff 1950 determined the composition of DNA ratios of adeninethymine and guaninecytosine were very close to 1 Rosalind Franklin and MH Wilkins conducted experiments on the xray diffraction of the DNA molecule James Watson and Francis Crick 1953 proposed a model for the structure of the DNA molecule based on the work done by Franklin and Wilkins They proposed the double helix structure DEOXYRIBONUCLEIC ACID DNA 1 DNA a polymer is made of two polynucleotide chains intertwined to form a double helix 2 Each nucleotide monomer contains a nitrogenous base which may be one of the o Purines adenine or guanine or o Pyrimidine thymine or cytosine 3 Each base is covalently linked to deoxyribose a 5C sugar 4 Deoxyribose is covalently bonded to a phosphate 5 The backbone of each single DNA chain is formed by alternating deoxyribose and phosphate groups joined by phosphodiester linkages 6 Each phosphate group is linked to the 5 carbon of one deoxyribose and to the 3 carbon of the other deoxyribose 7 Hydrogen bonds form between adenine and thymine two bonds and between guanine and cytosine three bonds The sequence of bases is complementary but not identical This allows to predict the sequence bases in one strand if one knows the sequence of bases in the other strand 8 Each pair base is 034 nm from the adjacent pair bases 9 There are ten base pairs in each turn of the helix making each turn 34 nm high 10 The double helix is 2 nm wide 11 The chains run in an opposite direction and are said to be antiparallel to each other At the end of each DNA molecule there is an exposed 5 carbon on one strand and an exposed 3 carbon on the other strand 12 Complementary base paring of adenine and thymine and guanine and cytosine are the basis of Chargaff s rule which is A T and C T in DNA DNA REPLICATION A process called replication can precisely copy DNA The essential features of DNA replication are universal but there are some differences between prokaryotes and eukaryotes due to the difference in DNA organization In prokaryotes DNA consists of a circular doublestranded molecule while in eukaryotes it is made of a linear doublestranded molecule associated with great deal of proteins The two strands of the double helix unwind Each strands serves as a template for the formation of a new complementary strand DNA replication is semiconservative each daughter double helix contains one strand from the parent DNA and one newly synthesized strand More than a dozen enzymes and proteins are involved in DNA replication MECHANISM 1 l P 9 DNA begins at specific sites in the molecule named origins of replication and forms the replication bubble Here at each end of the replication bubble DNA helicase creates a replication fork The position of the replication fork is constantly moving as replication proceeds The enzyme DNA helicase travels along the helix opening it as they move Helixdestabilizing proteins bind to the single DNA strands preventing reformation of the double helix Topoisomerases break and rejoin sections of the DNA to relieve strain and prevent knots during replication DNA synthesis always proceeds in a 5 3 direction 539 phosphate at one end and 339 hydroxyl at another end The two DNA strands are antiparallel that is their sugar phosphate backbones run in opposite directions DNA polymerases catalyze the linking together of the nucleotide subunits Nucleotides with three phosphate groups are used as substrates for the polymerization reaction Two of the phosphates are removed and the nucleotide is added to the 3 end of the growing strand These reactions are exergonic and do not require ATP DNA polymerase cannot initiate the synthesis of polynucleotide they can only add nucleotides to the 3 end of an already existing chain that is basepaired with the template strand DNA synthesis requires an RNA primer to initiate the synthesis reaction The RNA primer is made of about ten nucleotide long in eukaryotes The RNA primer is synthesized by a protein complex known as a primosome which includes an enzyme primase that is able to start a new strand of RNA opposite a DNA strand DNA replication is continuous in one strand and discontinuous in the other 15 DNA polymerase adds nucleotides to the 3 of the new strand that is always growing toward the replication fork This strand is called the leading strand 16 DNA polymerase adds nucleotides to the 3 of the new strand that is growing away from the replication fork This strand is called the lagging strand 17 Primase synthesizes a short RNA primer which is extended by DNA polymerase to form an Okazaki fragment 18 The lagging strand is synthesized in short pieces called Okazaki fragments which are made of 100 to 1000 nucleotides The fragments were discovered by Reijii Okazaki 19 These fragments grow in a direction away from the replication fork 20 Each Okazaki fragment begins with an RNA primer 21 After it has been elongated by DNA polymerase the RNA primer is degraded the gaps are filled with DNA and the adjoining fragments are linked together by DNA ligase 22 DNA ligase links the 3 end of one fragment with the 5 end of the adjoining fragment DNA replication is bidirectional starting at the origin of replication and proceeding in both directions An eukaryotic chromosome may have several origins of replication and may be replicating at several points at any one time ENZYMES REPAIRS ERRORS DNA polymerase proofreads each nucleotide against its template as soon as it is added If there is an error the nucleotide is removed and the correct one is added in its place Errors that arise after replication are also corrected Nucleotide excision repair 0 The mismatch pair of nucleotide distorts the DNA molecule 0 A nuclease enzyme cuts the damaged DNA strand at two points 0 The DNA is repaired by DNA polymerase by filling the gap with the correct nucleotides 0 DNA ligase attaches the new sequence to the rest of the molecule EUKARYOTIC CHROMOSOMES Replication results in the formation of a chromosome with two double helices Each double helix corresponds to a chromatid Eukaryotic chromosomal DNA molecules have special 39 called 39 at their ends These end caps of repetitive DNA are called telomeres Telomeres do not contain genes They are made of multiple repetitions of a nucleotide sequence e g TTAGGG is the repetitive unit in humans Recent research supports the idea that the repetitive DNA at the end of the chromosome has a protective function The number or repetitions in a telomere varies from 100 to 1000 A small amount of telomeric DNA fails to replicate each time the DNA replicates No essential genetic information is lost Telomeric DNA can be lengthened by a DNA replicating enzyme called telomerase Telomerase molecules have a small RNA molecule together with the protein Cells that produce telomerase continue to divide indefinitely beyond the point at which cell division would normally cease Active telomerase is found in germ cells that give rise to sperm and eggs in animals but it is absent in somatic cells The absence of telomerase activity in animal cells may be the cause of cellular aging It is possible that telomeres are a limiting factor in the life span of certain tissues ChapterS THE STRUCTURE AND FUNCTION OF MACROMOLECULES Small molecules have unique properties arising from the orderly arrangement of its atoms The major groups of biologically important molecules are carbohydrates lipids proteins and nucleic acids Usually they are very large containing thousands of atoms macromolecules Macromolecules are giant molecules formed by the union bonding of smaller molecules They consist of hundreds of thousands of atoms This is another level of biological organization POLYMERS Most macromolecules are polymers These are long chains formed by linking small organic molecules called monomers Polymerization is the linking together of monomers to form polymers It takes place through dehydration reactions 1 Condensation is the chemical process by which monomers are linked together A molecule of water is removed dehydration synthesis Each of the two monomers forming the bond contributes one part of the water molecule the hydroxyl group OH and the hydrogen H l Hydrolysis is the chemical process by which polymers can be degraded into monomers o A molecule of water is broken into H and OH and added to the broken bonds 0 Each molecular product receives a hydroxyl group or a hydrogen 0 Hydrolysis is the reverse of condensation dehydration synthesis A infinite number of polymers can be built from a limited number of monomers Each class of polymer e g lipids proteins etc is formed from a specific set of monomers 0 Proteins polymer are made of thousands of amino acid units monomer The uniqueness of organisms depends on the unique arrangement of the same monomers Macromolecules are constructed from only 40 to 50 common monomers and some others that occur rarely CARBOHYDRATES Carbohydrates include sugars and their polymers Carbohydrates contain carbon hydrogen and oxygen in a ratio of 121 or CH20n Monosacchan des are srrnpxe sugars They serve as suurees uf Energy and arbun aturns NurmaHy untammg 3 El 7 arbun aturns A hydraxy gruup rs banded tn eaen arbun Except une tn ugar ketune ketuse sugars G ucuse rs an amuse and truetuse a ketuse Mus t sugar narnes and m rose Dissacchan des are made uftvvu rnunusaeenange mm between twu rnunusaeenanges by a dehydratmn reaetruns They ean be spht by tne addmun ufvvaten hydrmyzed and tune truetuse G ucuse hnked tn ga amuse pruduces amuse tne sugar m m k Polysacchan des Repeatmg enarns uf rnunusaeenanges Smg e ung enarn ur branched enarn structures Surne rrnpurtant pu ysacchandes hnkages tnrs arrangernent makesthe staren mu ecme hehm o mylose rs tne srrnpxestturrn uf siarch rt rs Unbranched and hehm o Amylopectin rs a branched turrn vntn 17B hnkages at tne branch pmnt 0 MA lmkn D glucose 0 nuts Dgmcose branchpmms Amylopeclin model structure Suuree nttg vwwv sbu a ukWatErh sta htm Glycogen is made of glucose and is the storage carbohydrate of animals on 14 linkages o The glycogen molecule contains more branches than the amylopectin molecules o It is stored mostly in the liver and muscles Cellulose is also made of glucose monomers and is a structural carbohydrate 3 14 linkages o The angles of the bonds of the 3 14 linkages make every other glucose monomer quotupside downquot 9 Cellulose molecules are straight and never branched 9 Its hydroxyl groups are free to form hydrogen bonds with those of adjacent molecules 9 ln plant cell walls cellulose molecules form minute cables called microfibrils 9 Very few organisms can digest cellulose In most cases cellulose passes through the digestive tract and is eliminated in the feces Chitin is a polysaccharide used by arthropods in building the exoskeleton o The chitin monomer is a glucoselike molecule called Nacetylglucosamine in which an OH group is replaced by a chain of R NHCOCH3 group 9 When it becomes encrusted with calcium carbonate it becomes hard Chitin is also found in the cell wall of fungi insects spiders crustaceans and other animals 9 Some modified and complex carbohydrates have special roles LIPIDS Galactosamine is a structural carbohydrate present in cartilage it is amino derivative of galactose an enantiomer of glucose quot39 r 39 and g are 39 found on the outer surface of cells These are proteins with polysaccharide or fatty acid branches attached Lipids are diverse group of compounds made mostly of carbon and hydrogen with a few oxygen atoms found mainly in functional groups Hydrophobic molecules water repellent They are made mostly of hydrocarbons Soluble in nonpolar solvents For energy storage hormones structure of cell membrane Neutral fats phospholipids steroids waxes carotenoids and other pigments Storage lipids Fats are large molecules made from smaller molecules linked together by dehydration reactions Neutral fats are made of glycerol and three fatty acids Glycerol is a 3carbon alcohol Fatty acids are long unbranched hydrocarbon chain with a carboxyl group COOH at one end The carbon skeleton of the fatty acid usually has 16 to 18 carbon atoms At one end there is a carboxyl group that gives these molecules the name of fatty acids The nonpolarC H is the reason forthe 39 39 39 39 39 quot of the 39 39 39 When a fatty acid combines with a glycerol molecule a molecule of water is removed and an ester linkage is formed The fatty acids in a fat molecule may or may not be the same Triglyceride triacylglycerol is a synonym for fat Saturated fats have a maximum number of hydrogen atoms in the chain and are usually are solid at room temperature e g lard blubber and butter Unsaturated fats have double bonds between some of the carbon atoms and have less than the maximum number of hydrogen atoms Unsaturated fats have bends in the chains that prevent the aligning with the adjacent chain and prevent the van der Waals forces from acting They are usually liquid at room temperature e g vegetable oils Fats store at least twice as much energy as starch Humans and mammals store their fat in the adipose tissue of the body This tissue serves as a reservoir of energy as an insulator and cushions internal organs Structural lipids Phospholipids are major components of cell membranes Phospholipids differ from fats in having only two fatty acids instead of three and a phosphate group with a small additional molecule attached to the third carbon of glycerol instead of a hydroxyl group The hydrocarbon chains are hydrophobic but the phosphate group and its attached organic molecule e g choline lecithin are hydrophilic affinity for water 0 Amphipathic molecule Phospholipids form micelles and bilayers or double layers in aqueous solutions n m wuu awayfrum the Water 39 n a m Pr summen and the an pumt m the mtermr uf the membrane Cholesterol 5 a 512mm cumpunent uf eeH membranes uf amma s Hydruphubm Cuatmg mm and weave beeswax Earvvax same msects Functional fats ene enne Hngs Three was have swx camen amms and ene nas ve carbuns There are mnerent funmuna gruups attached m the was Tne engtn and siructure unne chem msungmsnes une stermd frum anutner leus msone and BE nmzrearn n e hnrrnnnp amma s aw n nng Cholesterol is a structural component of cell membranes but it is also a precursorfrom which other steroids are made Carotenoids are plant pigments involved in photosynthesis They are insoluble in water PROTEINS Proteins make more than 50 of the dry weight of most cells Proteins perform a variety of functions in the body structural support transport of other molecules body defense signaling between cells chemical catalysts called enzymes storage and other functions Proteins vary in their structure so they can perform specific functions Proteins are large complex molecules polymers of amino acids joined by peptide bonds These polymers are called polypeptides A protein is made one or more polypeptides folded and coiled into a specific conformation o 20 amino acids AA involved 0 Carbon hydrogen oxygen nitrogen and usually sulfur AA contain an amino group NH2 at one end and a carboxyl group COOH at the other end both attached to an alpha carbon 0 AAs have a variable side chain R group that determines the specific physical and chemical properties of each AA Except for glycine all other 19 amino acids used to synthesize proteins can exist as L or D enantiomorphs Only L amino acids are used for protein synthesis Bacteria and plants can synthesize all AA There are a few exceptions Animals synthesize some but not all AA Essential AA must be obtained from the diet Summarizing the four variable components of an amino acid alpha carbon amino group carboxyl group and the side chain AAs are usually ionized in the cell See Figure 517 on page 79 ofyour textbook The properties of the AA depend on the side chain 0 Nonpolar side chain makes the AA hydrophobic 0 Polar side chain makes the AA hydrophilic Negative side chain makes the AA acidic This is due to the presence of a carboxyl group in the side chain that is usually dissociated at the cellular pH Positive side chain makes the AA basic Both acidic and basic side chains are hydrophilic More httn39lusers rrn quot39 39 39 quot ma quot Bioloquaq quotquotquot quot html Peptide bond Two AA combine to form a dipeptide three form a tripeptide many form a polypeptide o The amino end of one AA joins the carboxyl end of the adjacent AA 0 An enzyme catalyzes the dehydration reaction The resulting covalent bond is called a peptide bond When this process is repeated thousands of times the resulting molecule is called a polypeptide Polypeptide chain may contain thousands of AA Polypeptide and protein are not synonymous Proteins consist of one or more polypeptide chains twisted into a unique shape The function of the protein depends on its ability to bind to another molecule Proteins have four levels of organization 0 Primary structure a unique sequence of AA for each polypeptide chain gt The sequence of AA is determined by inherited genetic information gt All proteins of a kind have the same AA sequence e g all lysozyme molecules gt A change in the sequence of AA is called a mutation 0 Secondary structure results from hydrogen bonds between H and O atoms of the backbone of the chain resulting in coiling or helix orfolding B pleated sheet The side chains atoms are not involved in the secondary structure of polypeptides o Tertiary structure is the overall shape of the polypeptide due to the interaction among the side chains R groups gt Hydrophobic interactions between side chains usually end up in the interior of the twisted polypeptide chain while hydrophilic side chains are exposed to the aqueous solutions gt Disulfide bridges are formed between the two sulfhydril groups of the AA cysteine This strong bonds gt Van der Waals forces ionic bonds and hydrogen bonds also contribute to the tertiary structure of the polypeptide chain 0 Quaternary structure is the relationship among several polypeptide chains of a protein These polypeptide chains become aggregated into a functional protein gt Fibrous proteins have several polypeptides coiled or aligned into ropelike structures gt Globular proteins are roughly spherical or compact The shape of the proteins determines its function Protein conformation depends also on the physical and chemical conditions of the environment like salt concentration temperature pH etc Changes in any of these conditions can cause the protein to unravel and become denatured Proteins become denatured become biologically inactive Scientists do not know little about the principles of protein folding Most proteins probably go through several intermediate stages before achieving its active conformation Chaperonins or chaperone proteins help in the proper folding of proteins but do not specify the conformation They protect the polypeptide from denaturing influences in the cytoplasm Xray crystallography is a method used in determining the three dimensional structure of a protein NUCLEIC ACIDS Encoded in the structure of DNA is the information that programs all the cell39s activities The DNA molecule contains hundreds of thousands of genes Genes determine the polymer sequence of AA in a protein Proteins are needed to implement what is in the genetic code in the DNA Two classes DNA deoxyribonucleic acid and RNA ribonucleic acid 0 Transmit hereditary information 0 Determine what the cells manufacture Nucleic acids are polymers that serve blueprints of proteins DNA is the genetic material that organisms inherit from their parents Flow of genetic information within the cell DNA a mRNA a protein DNA is located in the nucleus of the cell Protein synthesis takes place in organelles called ribosomes found in the cytoplasm of the cell Messenger RNA mRNA is synthesized in the nucleus following the DNA blueprint and then moves to the ribosomes with the message of about the protein to be synthesized Structure of nucleic acids Nucleic acids are polymers of nucleotides They are called polynucleotides A nucleotide is made of three parts an organic molecule called a nitrogenous base a pentose sugar 5C sugar and a phosphate group There are two groups of nitrogenous bases Pyrimiclines o 6 member ring of carbon and nitrogen atoms 0 Nitrogen atoms tend to take H from water and from there the name quotnitrogenous basequot is derived 0 Cytosine C thymine T and uracil U o Cytosine is found in both DNA and RNA thymine is found only in DNA uracil found only in RNA Purines Made of a sixmember ring fused to a fivemember ring Nitrogen and carbon make the rings Adenine A and guanine G Both are found in DNA and RNA 0 O O O Pentose sugars o Ribose is found in RNA and deoxyribose in DNA 0 They differ in the absence of an oxygen atom on the 2carbon of deoxyribose molecules 0 Deoxy without an oxygen The combination of a sugar with a nitrogenous base forms a nucleoside with an S and not a T The addition of a phosphate group to a nucleoside makes a nucleotide also known as a nucleoside monophosphate Nucleotides form polymers with the formation of a covalent bond between the phosphate on one nucleotide and the sugar of the next These covalent bond are of a kind called phosphodiester bond The resulting polymer forms the backbone that will make the DNA or RNA molecule The nitrogenous bases stick out to the side of the backbone The pentose sugar in RNA is ribose and in DNA is deoxyribose o The carbons in these sugars are numbered and a prime afterthem eg the second carbon is written as 2 two prime 0 The carbon that stick up from the ring is the 5 carbon The phosphodiester linkages occur between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 of the next The two free ends of the backbone chain are different from each other One end has a phosphate attached to a 5 carbon and the other has a hydroxyl attached to 3 carbon We refer to these as the 5 and the 3 ends of the strand Only certain bases are compatible to establish the required hydrogen bonds In other words the two strands of a double helix are complementary o Adenine always pairs with thymine a purine with a pyrimidine o Guanine always pairs with cytosine If a strands has the sequence ATGGCAACC its complementary strand will be TACCGTTGG The complementarity of the strands makes it possible to make an accurate copy of each of the two strands and therefore of the genes The linear sequence of bases is passed from parents to offspring Closely related individuals have greater similarity in their DNA and proteins than unrelated individuals Closely related species will share a greater portion of their DNA than distantly related species The sequence of nucleotides in these polymers is limitless and so is the number of nitrogenous bases forming the side branches Genes are made of hundreds of nucleotides Double helix and inheritance The RNA molecule consists of a single polynucleotide chain The DNA molecule is made of two polynucleotide chains or strands forming a double helix The two sugarphosphate backbones run in opposite 5 a3 directions from each other an arrangement referred to as antiparallel 5 ATGGCAACC3 3 TACCGTTGG5 The strands are held together by hydrogen bonds and van der Waals forces established between facing nitrogenous bases Summary of chapter5 in this site httpwww quot 39 39 hi stat 39 39 39 quot1R htm 1 Macromolecules of life carbohydrates lipids proteins and nucleic acids 2 Polymers and polymerization o Monomers o Dehydration reactions 0 Condensation reactions Hydrolysis 3 Carbohydrates 0 Structure carbon hydrogen and oxygen in a ratio of 121 or CHZO 0 Include sugars and polymers of sugars o Monosaccharides adoses and ketoses ring form in aqueous solutions 0 Polysaccharides glycosidic linkage 0 Storage polysaccharides starch amylose amylopectin and glycogen 0 Structural polysaccharides cellulose and chitin 4 Lipids 0 Structure carbon and hydrogen with a few oxygen atoms found mainly in functional groups 0 Hydrophobic 0 Fat structure glycerol ester linkage fatty acids 0 Fatty acid structure hydrocarbon carboxyl group saturated unsaturated o Phospholipids hydrophilic head hydrophobic tail 0 Steroids skeleton of four fused rings 5 Proteins 0 Structure polymer of amino acids 0 Peptide bond learn the structure of the peptide bond and it is formed 0 Polypeptides o Conformation determines how it words enzymes 0 Four levels of protein structure 0 Primary unique sequence of AA 0 Secondary repeated portions of coils and folds alpha helix pleated sheets 0 Tertiary formed by the interactions of side chains of the AA that causes three dimensional structures ionic and H bonds disulfide bridges van der Waals interactions 0 Quaternary overall structure of the protein due to the aggregation of several polypeptide subunits Folding and denaturing of proteins 6 Nucleic Acids DNA and RNA Polymers of monomers called nucleotides Nucleotides structure sugar phosphate and nitrogenous base Two sugars ribose and deoxyribose Four nitrogenous bases 0 Purines have two rings adenine and guanine o Pyrimidines have one ring cytosine and thymine or uracil in RNA DNA double helix Base pairing C G and A T Sample test September 10 2004 I Multiple choice PRINCIPLES OF BIOLOGY Test 1 Ch 14 Name 40 points UPN neovee F A 5339 wepvww wepvwm 999579 oguoo apvew Which is the best description of the science of biology The study of life The study of rocks The study of humans The study of biodiversity The study of the way humans interact with their environment A maple leaf is at which level in the hierarchical organization of life Tissue c Organ e Organelle Population d Organism Which of the following is the main source of energy for producers such as plants 39 M39 s LIght c Carbon dioxide d Inera Heat d Chemicals energy Feedback mechanism Homeostasis c Evolution d Cellular respiration What are the two classifications of prokaryotes Domain bacteria and Domain Eukarya Domain archaea and Kingdom Monera Domain Eukarya and domain Archaea Domain Bacteria and Kingdom Monera Domain Bacteria and Domain Archaea A rose bush is classified into Domain and Kingdom EukaryaAnimalia EukaryaFungi EukaryaPlantae EukaryaProtista BacteriaArchaea Which of these provides evidence of the common ancestry of all life The ubiquitous use of catalysts by living systems The universality of the genetic code The structure of the nucleus The structure of cilia The structure of chloroplasts When applying the process of science which of these is tested A question c A result e An observation A prediction d A hypothesis Which of the following utilizes DNA in their genetic material Prokaryotes Eukaryotes Archaea A and C only e Photosynthesis What name is given to the process by which plants convert the energy of light to chemical 999579quot 3999579quot 4 0905794 0995 4 999579quot 0995 5105794 2 3 4 5 A Band C When two atoms are equally electronegative they will interact to form Equal numbers of isotopes lons Polar covalent bonds Nonpolar covalent bonds lonic bonds The ionic bond of sodium chloride is formed when Chlorine gains an electron from sodium Sodium and chlorine share an electron pair Sodium and chlorine both lose electrons from their outer valence shells Sodium gains an electron from chlorine Chlorine gains a proton from sodium Oxygen has an atomic number of 8 Therefore it must have 8 protons 8 electrons 16 neutrons Only A and B are correct A B and C are correct In a single molecule of water the two hydrogen atoms are bonded to a single oxygen atom by Hydrogen bonds Nonpolar covalent bonds Polar covalent bonds lonic bonds Van der Waals interactions What determines the cohesiveness of water molecules Hydrophobic interactions High specific heat Covalent bonds Hydrogen bonds lonic bonds Electrons exist only at fixed levels of potential energy However if an atom absorbs sufficient energy a possible result is that An electron may move to an electron shell farther out from the nucleus The atom may become a radioactive isotope An electron may move to an electron shell closerto the nucleus The atom would become a positively charged ion The atom would become a negatively charged ion Organic chemistry is the branch of chemistry that studies biochemical processes physiological processes oxygen compounds carbon compounds e none of the above 17 Compare these two isotopes of phosphorus one has an atomic mass of 31 and the other an atomic mass of 32 This difference depends on a A different atomic number b One more neutron c One more proton d One more electron e A different charge 18 Which of these statements is true of all anions a The atom has more electrons than protons b The atom has more protons than electrons c The atom has fewer protons than does a neutral atom of the same element d The atom has more neutrons than protons e The net charge is 1 19 There is unity in the diversity of life This unity is evident in a The universal genetic code b Similar metabolic pathways or cell functions c Similar cell structure d A and B only are correct e A B and C are correct 20 Weak temporary attractions between atoms and molecules are called a Polar bonds c Nonpolar bonds e Covalent bonds b lonic bonds d Van der Waals interactions ll Fill in the blanks 44 points 1 The branch of science that deals with living organisms and vital processes 2 Organisms made of a single cell 3 Level of hierarchical organization above the organism level Organisms of the same kind that are genetically very similar and can breed in the wild or without human interference and produce live fertile offspring 4 Cell type with a circular DNA without free ends 5 Name the science of classifying organisms 6 ln chemistry a substance consisting of two or more elements combined in a fixed ratio is called aan 7 Name the chemical bond formed when two atoms share electrons 8 What bonds are broken when water vaporizes are O A O A A 19 A NH3 H lt gt NH4 therefore ammonia is a The thermometer is used to measure the Water can cling to molecules of other substances that are polar or partially polar This is called The energy of motion is called The amount of energy required to raise the temperature of 1gram of a substance 1 C is called is a homogeneous mixture of two substances The dissolving agent is called the The substance that is dissolved is the l repel water Solutions resist changes in pH when acids or bases are added are called because it accepts a energy of the molecules Molecules made of only carbon and hydrogen atoms are called Name given to isomers that are mirror images of each other Usually one form is biologically active and the other is not Amines are organic compounds having the functional group called lll True orfalse Make sure the T39s and F39s are clearly distinguishable 7 points Ecosystem dynamics includes two major processes nutrient cycling and energy flow Species are static and do not change over time Cells are the units of structure and function of living things Weight is the amount of matter an object has Electrons can change from one energy level to another unoccupied level by gaining or loosing energy The chemical behavior of an atom depends on the valence electrons The reactivity of atoms arises from the presence of unpaired electrons in one or more orbitals of their valence shells Extra points Write the structural formula of the following functional groups 1 Carboxyl group 2 Aldehyde 3 Phosphate What is the name of the following functional groups 1 ChapterB A TOUR OF THE CELLS All organisms are made of cells Cells are the units of structure and function There are singlecell organisms called unicellular organisms and manycelled organisms called multicellular organisms HOW WE STUDY CELLS The cell is the simplest level of organized matter capable of life functions capable of living All cells are related by their descent from earlier cells but they have been modified in various ways during their long evolutionary history Microscopy Microscopes are the most important tools of cytology the study of cell structure Light or compound microscope Visible light passes through a specimen and lenses The lenses refract bends light and the image is enlarged Good for magnifying objects up to 1000x Resolution or resolving power is the ability to distinguish fine detail Minimum distance between two points that can be seen separately 0 Magnification is the ratio of an object s image to its real size Most cells range between 1 and 100 pm in diameter and can be seen only with the aid of a microscope Most cell organelles are too small to be resolved by the light microscope The micrometer is the unit normally used to measure cells 0 1 pm 1 millionth of a meter 10396 or1 thousandths of a millimeter 0001 ml Remember the equivalence of these units of length in the metric system See Appendix B and C Campbell text Starting with the meter the mm um and nm are 0001 of the previous unit 0 1 meter m 328 feet 109 yards o 1 millimeter mm 10393m o 1 micrometer pm 10393 mm 1O396m o 1 nanometer nm 10393pm 109 m Fluorescent microscopes are used to detect the location of certain molecules in the cell Fluorescent stains dyes and antibodies absorb light of short wavelength and UV radiation and release light of another wavelength The emitted light allows observing the location of the molecules and the structures to which they are bound Computing imaging methods have improved the resolution of structures labeled by fluorescent dyes Electron microscopes Most subcellular structures are too small to be seen with the compound microscope Energized electron beam is focused by electromagnets through the specimen or onto its surface Electron beams have wavelengths much shorter than visible light The term cell ultrastructure refers to the cell anatomy as seen with the electron microscope 1 Transmission electron microscope TEM Magnification 200000x or more The electron beam passes through the specimen and is projected on a fluorescent screen or photographic plate Electromagnets instead of prisms to focus and magnify the image onto a screen It is used to study the internal structures of the cell 2 Scanning electron microscopes SEM Magnification 3000 to 100000x o The specimen is coated with metal The electron beam strikes the metal and dislodges electrons from the metal coat These electrons are then focused onto a screen 0 The intensity of these electrons varies with the contour of the surface and gives a three dimensional figure of the surface It is used to study the surface of the specimen Microscopes reveal the structure of the cell but not its function Modern cell biology integrates cytology and biochemistry in order to understand the relationship between structures and functions of organelles Organelles can be isolated Cell fractionation is a method of purifying organelles and separating them from other cell structures in orderto study their individual functions This is an example of reductionism in biology Centrifuges of different types are used to fractionate cells The most powerful centrifuges are the ultracentrifuges that can spin at 130000 revolutions per minute rpm Cells are broken up homogenization and the mixture is centrifuged into the pellet and the supernatant In differential centrifugation the supernatant is spun at successively higher speeds in order to separate the components on the basis of their different sizes and densities o The pellet contains the heavier structures of the cell and become packed at the bottom of the test tube The supernatant contains the liquids and the suspended lighter structures of the cell 0 The supernatant is decanted into another test tube and centrifuged again at a higher speed 0 This process is repeated several times at increasing higher speeds collecting pellets containing lighter and lighter structures CELL STRUCTURES A PANORAMIC VIEW All organisms are made of one of two structurally different cells prokaryotic and eukaryotic cells From the Greek 0 Pro before karyon kernel 0 Eu true karyon kernel EUKARYOTIC CELLS PROKARYOTIC CELLS Have a nuclear membrane nucleus Lack a nuclear membrane nucleoid Have two to hundreds of chromosomes Have a single chromosome and plasmids DNA is double helix DNA in a single circular strand Have membranebounded organelles Lack membranebounded organelles Large ribosomes 80S Small ribosomes 70S Sexual reproduction by fusion Sexual reproduction unknown Asexual reproduction by mitosis Asexual reproduction by fission Prokaryotic cells are simpler than eukaryotic cells Prokaryotic cells are considered to be more primitive than eukaryotic cell Prokaryotic cells have their DNA concentrated in a region called the nucleoid but there is no membrane separating the nucleoid region from the rest of the cell Eukaryotic cells have highly organized membranebounded organelles Nucleoplasm is the term used for the material inside the nuclear membrane Cytoplasm refers to the part outside the nucleus of the cell This term is also used for the material inside prokaryotic cells Organelles are suspended on the cytosol of the cytoplasm Organelles have specialized structures and functions