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Principles of Biology I

by: Sadye Osinski Sr.

Principles of Biology I BIOL 111

Marketplace > Christian Brothers University > Biology > BIOL 111 > Principles of Biology I
Sadye Osinski Sr.

GPA 3.63

Arthur Salgado

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Arthur Salgado
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This 62 page Class Notes was uploaded by Sadye Osinski Sr. on Monday October 5, 2015. The Class Notes belongs to BIOL 111 at Christian Brothers University taught by Arthur Salgado in Fall. Since its upload, it has received 149 views. For similar materials see /class/219442/biol-111-christian-brothers-university in Biology at Christian Brothers University.


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Date Created: 10/05/15
Chapter22 INTRODUCTION OT DARWINIAN EVOLUTION Evolution is the cumulative changes of inheritable characteristics over time Population is a group of individuals of the same species living in an area Heritable traits are those that can be passed on to offspring IDEAS ABOUT EVOLUTION BEFORE DARWIN 1 Aristotle 384322 B C Greek philosopher Aristotle proposed that the last stage of development the adult form explains the changes that occur in the immature forms teleological explanation the advanced stages influence the earlier stages He also proposed that all living forms are linked in a progression from imperfect to most perfect He called this the Scale of Nature 2 Natural theology The Creator made the individual species In the 170039s biology was dominated by natural theology A philosophy dedicated to discovering the plan of the creator by studying nature Natural theologians saw the adaptations of organisms as evidence that the Creator had designed each and every species for a particular purpose 3 Hutton James 172697 Scottish geologist Hutton formulated controversial theories of the origin of the earth in 1785 He was of the opinion that the earth must be very old Uniformitarianism the doctrine that past geological changes in the earth were brought about by the same causes as those now taking place It stressed the slowness and gradualness of rates of change 4 Cuvier Georges L opold Chr tien Fr d ric Dagobert Baron 17691832 French naturalist Cuvier originated a system of zoological classification based on structural differences of the skeleton and organs Catastrophism the geological doctrine that the physical features of the earth39s surface eg mountains and valleys were formed during violent worldwide cataclysms eg earthquakes and floods He argued that all living things were destroyed and replaced with wholly different forms during these cataclysmic events 5 Lyell Sir Charles 17971875 English geologist Lyell argued in this book that at the time presently observable geological processes were adequate to explain geological history He thought the action of the rain sea volcanoes and earthquakes explained the geological history of more ancient times Lyell conclusively showed that the earth was very old and had changed its form slowly mainly from conditions such as erosion Lyell was able to date the ages of rocks by using fossils embedded in the stone as time indicators Lyell helped win acceptance of James Hutton39s theory of uniformitarianism and of Charles Darwin39s theory of evolution 6 Lamarck Jean Baptiste Pierre Antoine de Monet Chevalier de 17441829 French naturalist Lamarck proposed that organisms evolve into new species He thought that all organisms are tied together by intermediate evolutionary forms and that species distinctions are manmade and arbitrary He thought that all organisms were endowed with a vital force that drove them to change toward greater complexity over time Lamarck thought that organisms could pass acquired characteristics to their offspring Charles Darwin 18091882 0 Charles Robert Darwin was born in Shrewsbury England in 1809 The son of an eminent local doctor Dr Robert Darwin Charles was born into a modestly wealthy family 0 He was the grandson of Erasmus Darwin English naturalist and promoter of the idea of evolution 0 Darwin studied medicine at Edinburgh University from 1825 to 1827 0 He transferred to Christ39s College Cambridge in 1828 with the intention of becoming a minister in the Church of England 0 He was a mediocre student and did not like classical education His interests were in natural history botany geology collecting and hunting o In 1831 with the help of his botany professor John Henslow and his uncle Josiah Wedgewood he took the post of naturalist on board the HMS Beagle on a scientific mission to South America 0 By the time of his return in 1836 he had become an authority on many forms of life 0 Between 1842 and 1844 he developed his theory of natural selection although he did not announce his work until 1858 o In 1859 he published a considerably expanded version of his researches in the controversial Origin of Species by Means of Natural Selection 0 He published The Descent ofMan in 1871 THE VOYAGE OF THE BEAGLE HMS Beagle under the command of Captain Robert Fitzroy left for Patagonia South America in 1831 with Charles Darwin on board At this time Charles did not believe in evolution including his grandfather s theory as any evidence presented so far could not convince him The Beagle reached South America in 1832 and Charles took care to observe the flora and fauna Charles went then to Buenos Aries where he saw fossils of more ancient animals including a mastodon He experience a violent earthquake in Chile that raised the land in some places between 2 and 10 feet Darwin was most interested in the plants and animals on the Galapagos a group of 16 large islands and many smaller off the coast of Ecuador 0 Giant tortoises inhabit every one of the islands which gave the island chain its name from the Spanish Galapagos meaning tortoise 0 Each island has its own type of tortoise distinguishable by the shape and pattern of its shell 0 Darwin was astonished that the islanders felt that this was due to the difference in environment on each island 0 Darwin also observed the finches which varied in size and shape from island to island 0 Their beaks also varied depending on which food they ate and some even had extra long tongues for grabbing certain types of foods such as insects nuts or seeds lsland animals and plants were different to those on the mainland but a relationship could be seen What was even strangerthough to Darwin was the fact that organisms on different islands varied but still seemed related THE MECHANISM OF NATURAL SELECTION Charles Darwin and Alfred Wallace independently proposed a mechanism that brings about the evolution of populations The mechanism by which the organisms best suited to survival pass on theirtraits to the next generation The mechanism is based on the following observations and inferences 1 Overproduction of offspring o All species have great potential fertility Without constraints populations will grow exponentially producing an ever more rapidly growing number of organisms 2 Population remain stable 0 In spite of this prediction the numbers of individuals in a population remains near equilibrium fluctuating above and below some mean value 3 Resources are limited 0 Production of more individuals that the environment can support 0 Resources are limited This results in a struggle for existence 0 Organisms compete for these limited resources There is a struggle for existence 0 Survival of a fraction each generation INFERENCE Production of more individuals that the environment can support results in a struggle for existence resulting in a fraction of the population surviving each generation 4 Variation 0 Individuals are unique There is individual variation This came from observing animal breeding 5 Much of this variation is inheritable Much but not all of the individual variation is heritable This observation also came from animal breeders The next generation obtains the parents heritable traits Best adapted individuals reproduce most successfully Some of the observed variation is environmental some is genetic Darwin and Wallace did not know the mechanism of inheritance They had not read Mendel s paper INFERENCE Reproductive success Some individuals are better equipped to survive and reproduce They have inherited traits that make them best fit to survive in their environment INFERENCE This unequal ability to reproduce will lead to a gradual change of the population with favorable characteristics accumulating over time It is useful to distinguish Darwin39s mechanism of natural selection from evolution generally Darwin and Wallace s contribution was not the hypothesis of evolution but a description of the mechanism by which evolution takes place Other naturalists such as Lamarck and Darwin39s grandfather Erasmus Darwin anticipated him in this respect Natural selection is often described as quotsurvival of the fittestquot it maintains that the organisms best suited to survive in their environment are more likely to reproduce and pass their genetic material to the next generation while those with less advantageous traits are less likely to survive long enough to reproduce Darwin used quotdescent with modificationquot According to Darwin the diversity of life forms have arisen by descent with modification from ancestral species Darwin illustrated the power of selection as a force in evolution with examples from artificial selection the breeding of domesticated animals and plants Humans have modified many species by the selective breeding of individuals with preferred traits The evolution of insecticide resistant insects antibiotic resistant bacteria and herbicide resistant weeds illustrate the process of selection and the gradual change in a population Darwin39s main ideas A Natural selection is differential success in reproduction 2 Natural selection occurs through the interaction between the environment and the variability found in a population 3 The product of natural selection is the adaptation of populations of organisms to their environment SUPPORTING EVIDENCE COMPARATIVE ANATOMY Structures with a similar underlying plan can be explained by relationship through common ancestry 1 Homologous vs analogous Homologous features are variations of the same basic structural pattern even though the structure may be used differently I are a 39 to indicate evolutionary affinity among organisms possessing them Homoplastic or analogous features have similar function but lack the basic pattern of homologous structures eg wings of birds and insects Homoplastic features shown what is called convergent evolution It is due to the selection for similar habitats in different evolutionary lineages Adapting organisms carry structures that are no longer necessary These structures are nonfunctional and degenerate remnants of structures that were functional in ancestral organisms These reduced structures are called vestigial 2 Embryological homologies Homologies exist between developing embryos Sometimes homologies are evident in the developing embryo but not in the adult organism There is a remarkable similarity between vertebrate embryos embryological homologies Embryos begin with similar gill arches or pouches and a similar vertebral column that becomes modified in later stages to yield the various different forms characteristic of the organisms 3 Molecular homologies There are molecular homologies eg the structure of DNA and RNA the process of replication transcription and translation pathway of cellular respiration and the genetic code Lines of descent based on molecular characters closely resemble lines of descent based on structural and fossil evidence The universality of the genetic code is considered to be an evidence that all organisms have a common ancestor Amino acid sequence in common proteins reveals greater similarities in closely related species A greater proportion of nucleotide sequence in DNA is identical in closely related organisms The universal genetic code and many pathways glycolysis Krebs cycle photosynthesis etc support a common origin THE TREE OF LIFE Homologies that arose recently are shared by a smaller branch of the tree of life Those that arose very early are shared by many and more diverse groups of organisms 4 Biogeography or geographical distribution Closely related species tend to be found in the same geographic area Same ecological niches found in distant lands are occupied by very different though superficially looking species e g Australian marsupials and Eurasian placental mammals Geographical barriers lead to great differences between organisms eg adaptive radiation of Australian marsupials lsolation tends to produce endemic species 0 Endemic endemism refer to species native and restricted to a geographical region 5 Fossils The fossil record shows a general progression from the earliest singlecelled organisms to organisms living today Some fossils appearto be intermediates between living groups e g Archaeopteryx evolution of the horse a Coelacanth The fossil record is incomplete Radioactive isotopes found in fossils and rocks provide a means of measuring the age of the fossil or rock layer EXPERIMENTAL DATA Some experiments show that populations change over time due to some environmental pressure Reznick and Endler have studied the evolution of guppy populations in streams where predation was high and in others where predation was low They designed an experiment where similar guppy populations were subjected to high and low preda Ion Predation exerted a selective pressure on the guppy population quot There is grandeur in this view of lifequot Darwin closing line of the Origin of the Species Chapter 19 VIRUSES Viruses are subcellular particles that cannot metabolize on their own and are not considered to be truly living organisms Viruses consist of nucleic acid enclosed in a protein coat and sin some cases a membranous envelope A virus is a genome enclosed in a protective coat Viruses are infectious agents and are not assigned to any of the six kingdoms Viruses are organized associations of macromolecules Viral genomes capsids and envelopes 0 Nucleic acid DNA or RNA which carries the blueprint for the replication of progeny Viruses o The genomes may consist of a double stranded DNA a single stranded DNA a double stranded RNA or a single stranded RNA The smallest virus has only four genes the largest viruses have several hundreds Contained within a protective shell of protein units called the capsid The capsid could be made of a single type of protein or of several hundred types of proteins The capsids may have a variety of shapes rod shaped polyhedral spherical etc 0 Some viruses have viral envelopes membranes that coverthe capsid and help them to infect their hosts 0 Viral envelopes are derived from the host cell and it contains host cell phospholipids and membrane proteins Viruses cannot replicate outside of a living cell Once it has invaded a cell it is able to direct the host cell machinery to synthesize new intact infectious virus particles virions Because viruses are nonmotile they are entirely dependent on external physical factors for chance movement and spread to infect other susceptible cells Viruses are between 20 and 300 nanometers long The genome DNA or RNA codes for the few proteins necessary for replication 0 Some proteins are functional eg nucleic acid polymerases o and some are structural ie they become incorporated and form part of the virion Phages or bacteriophages are viruses that attack bacteria cells Phages have the most complex capsids They have a polyhedral head a tail piece and fibers for attachment to the bacterium Classification 1 Viruses are broadly classified primarily upon the type of genomic nucleic acid eg DNA or RNA 2 Then further by the number of strands of nucleic acid eg doublestranded DNA double stranded RNA or singlestranded RNA 3 Retroviruses are a special category of RNA viruses that require reverse transcription of their RNA to DNA and then integration of that DNA into the host cell genome before replication and transcription can take place They carry a reverse transcriptase enzyme as part of the virion Viruses infect humans animals plants and other organisms In humans they are responsible for chickenpox mononucleosis herpes mumps warts influenza hepatitis AIDS certain types of cancer etc REPRODUCTION Viruses lack enzymes ribosomes and other equipment for making proteins Each type of virus can infect only a limited range of host cells called its host range The host specificity depends on the recognition system of the virus for the identification of the host cell A virus reproductive cycle could be lytic or temperate Lytic cycle 1 Attachment to the host cell using its tail fibers to stick to specific receptor sites on the host39s membrane 2 Penetration of the nucleic acid into the cytoplasm of the cell 9 Bacterial DNA is destroyed replication of viral macromolecules 4 Cell39s metabolism is directed by the viral genome 5 Assembly of the newly synthesized viral components viral nucleotides proteins etc 6 Release of the new viruses by destroying the host cell with lytic enzymes lysozymes Temperate or lysogenic cycle The phage injects the DNA into the host cell The viral DNA is incorporated into the hosts DNA and the viral genome is replicated along with DNA of the host cell This DNA is no known as a prophage When the bacterium divides the daughter cells receive the inserted viral DNA Bacterial cells carrying prophages are called lysogenic cells Lysogenic cells may exhibit new properties The virulence of bacteria that causes diphtheria botulism and scarlet fever is due to prophage genes that make the bacteria produce toxins Occasionally a prophage exits the bacterial chromosome and initiates a lytic cycle Animal viruses Animal viruses often have an envelope made from the host39s cell membrane which allows them to enter or exit the cell Retroviruses are a special category of RNA viruses that require reverse transcription of their RNA to DNA and then integration ofthat DNA into the host cell genome before replication can take place They carry a reverse transcriptase enzyme as part of the virion 0 HIV human immunodeficiency virus is a retrovirus Vaccines are harmless variants or derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen Effective vaccines have been developed against many viral diseases e g polio smallpox mumps hepatitis and rubella German measles Emergent diseases are those that were not known before or that have been absent for at least 20 years 0 Emerging infectious diseases are diseases of infectious origin whose incidence in humans has increased within the past two decades or threatens to increase in the near future 0 Ebola virus HIV hantavirus Many factors or combinations of factors can contribute to disease emergence Newly emergent infectious diseases may result from 0 changes or evolution of existing organisms 0 known diseases may spread to new geographic areas or new human populations previously unrecognized infections may appear in persons living or working in areas undergoing ecological changes such as deforestation or reforestation that increase their exposure to insects animals or environmental sources that may harbor new or unusual infectious agents The great influenza epidemic of 1918 killed between 30 and 40 million people around the globe o It probably is the largest loss of life from an individual disease in a single year Highdensity population increases the chance of contamination and infection due to increase contact pollution and lack of hygiene Emerging infections such as acquired immunodeficiency syndrome AIDS and TB vividly illustrate that no nation can be complacent regarding human vulnerability to the microorganisms with which we share our environment Since the early 1970s the US public health system has been challenged by many newly identified pathogens and syndromes such as Lyme disease Legionnaires39 disease toxic shock syndrome human immunodeficiency virusAIDS hepatitis C virus cryptosporidiosis and most recently hantavirus Examples of Emerging Infectious Diseases United States 1993 E coli O157H7 disease Cryptosporidiosis Coccidioidomycosis Multidrugresistant pneumococcal disease Vancomycinresistant enterococcal infections Influenza ABeijing3292 Hantavirus infections Examples of Emerging Infectious Diseases Outside the United States 1993 Cholera in Latin America Yellow Fever in Kenya Vibrio cholerae 0139 in Asia E coli O157H7 in South Africa and Swaziland Rift Valley Fever in Egypt Multidrugresistant Shigella dysenteriae in Burundi Dengue in Costa Rica Diphtheria in Russia Antibiotic and pesticide resistance strains have appeared in many parts of the world Natural selection and the ability of many organisms to evolve new forms are responsible for the emergence of many diseases that were under control a few years ago Tumor viruses Tumor viruses insert their DNA in the host cell39s DNA triggering cancerous changes through their own or host cell39s genes The virus responsible for hepatitis B also seems to cause liver cancer in individuals with chronic hepatitis Viral genes that directly cause cancer are called oncogenes Protooncogenes are found in normal cells and produce proteins associated with the cell cycle In some cases the virus transforms the cell by turning on or increasing the expression of the cell39s oncogenes Plant viruses Plant viruses cause much damage to agriculture Most plant viruses are single stranded RNA viruses The viruses may enter the plant through damaged cell wall or could be inherited from a parent during asexual propagation Viruses may have evolved from cell fragments containing DNA and that were able to move from one cell to another VIROIDS AND PRIONS A viroid consists of a short circular strand of RNA with no protein coat They are made of several hundred nucleotides Viroids do not encode proteins but can replicate in host plant cell and disrupt the metabolism of the entire plant Prions are small polypeptide chains consisting of 208 amino acids They are abnormal versions of normal brain proteins When prions contact a similar protein it may induce the normal protein to adopt an abnormal shape A chain reaction will follow until the prions reach a dangerous level causing cellular malfunction and possibly degeneration of the brain These particles have been associated to animal and plant diseases httpwww kmm quot 39quot 39 lainu WebsiteLectsPRIONSHTM 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 Cercozoans or 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 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 Chapter 18 REGULATION OF GENE EXPRESION Only certain portion of the genetic information is expressed in a cell Genes are regulated in several ways 1 By controlling the amount of mRNA that is available 2 By controlling the rate of translation of the m RNA 3 By controlling the activity of the protein product BACTERIA REGULATES TRANSCRIPTION Cells can adjust the activities of enzymes already present Cells can adjust the production levels of certain enzymes by controlling the amount of mRNA that is transcribed The basic mechanism for this control of gene expression in bacteria is called the operon model The French scientists Francois Jacob and Jacques Monod at the Pasteur Institute in Paris discovered the operon model OPERON THE BASIC CONCEPT Genes of related functions can be grouped into one transcription unit A single onoff switch can control the whole cluster of functionally related genes The switch is a segment of DNA called the operator The operator is a sequence of bases that overlaps the promoter and serves as the regulatory switch responsible for transcriptional level control of the operon Most regulated genes in bacteria are organized into operons Operons permit coordinated control of functionally related genes An operon may encode for several proteins Each protein encoding sequence of an operon is called a structural gene Each operon has a single promoter region upstream from the protein coding regions The promoter is the DNA sequence to which the RNA polymerases attach The operator is positioned within the promoter or in between the promoter and genes it controls All together the operator the promoter and the genes they control constitute an operon The entire stretch of DNA required for enzyme production Repressor genes encode repressor proteins Repressor proteins bind speci cally to the operator sequence and block transcription by preventing RNA polymerase from binding to the promoter Some repressor may always be on thus repressing the eXpression of a gene in a cell The repressor is the product of a regulatory gene which is located some distance from the operon it controls and has its own promoter Regulatory genes are eXpressed continuously The binding of repressors to operators is reversible A repressible operon is usually turned on They are turned off under special conditions when a repressorcorepressor compleX is bound to the DNA operator The repressor protein is synthesized in an inactive form that cannot bind to the operator A metabolite often an end product acts as a corepressor that binds to the allosteric site of the repressor protein When the supply of the end product corepressor is low all enzymes in the pathway are actively synthesized and the repressor cannot bind to the operator The metabolite corepressor and the protein repressor must come together to repress the gene REPRESSIBLE AND INDUCIBLE OPERONS TWO TYPES OF NEGATIVE GENE REGULATION Repressible operons are usually on but can be inhibited repressed when a speci c small molecule binds allosterically to a regulatory protein Inducible operons are usually turned off but can induced or stimulated when a small molecule interacts with a regulatory protein 1 Inducible genes 0 Repressor protein alone turns off regulated genes 0 Repressor protein plus inducer inactivate the repressor and the gene continuous to transcribe o The inducer represses the repressor 2 Repressible genes 0 Repressor protein alone cannot turn off regulated genes 0 Repressor protein and corepressor turn off the regulated gene Inducible enzymes are synthesized induced by chemical signals Repressible enzymes function in anabolic pathways which synthesize end products from raw materials The production of the end product is suspended when there is enough material produced POSITIVE REGULATORS Some inducible operons are under positive control Positive controls operate through an activator protein catabolite gene activator protein or CAP CAP increases the af nity of the promoter for RNA polymerases It allows the enzyme to recognize the promoter ef ciently and to bind tightly to the DNA The active form of CAP has cAMP bound to an allosteric site cAMP is a coactivator Activator protein CAP alone cannot stimulate transcription or regulated genes Activator protein and coactivator CAP cAMP stimulate transcription of regulated gene EUKARYOTIC GENE EXPRESSION All cells in the body have the same genome Human cells eXpress about 20 of its genes Highly differentiated cells like nerve and muscle cells eXpress an even smaller fraction of its genes The genes eXpressed in each cell type are unique The differences between cell types are due not to different genes being present but to differential gene expression 1 REGULATION OF CHROMATIN STRUCTURE The structural organization of chromatin not only packs a cell s DNA into a compact form that ts inside the nucleus but also helps regulate gene eXpression in several ways The location of a gene s promoter relative to nucleosomes and to the sites where the DNA attaches to the chromosome scaffold or nuclear lamina can affect whether the gene is transcribed Genes with heterochromatin which is highly condensed are usually not eXpressed 2 IHSTONE MODIFICATIONS There is evidence that chemical modi cations to histones the proteins around which the DNA is wrapped in nucleosomes play a direct role in the regulation of gene transcription The Nterminus of each histone molecule in a nucleosome protrudes outward from the nucleosome These histone tails are accessible to various modifying enzymes In histone acetylation acetyl groups COCH3 are attached to lysine s in histone tails When lysine s are acetylated their positive charges are neutralized and the histone tails not longer bind to neighboring nucleosomes Methyl group and phosphate groups can be reversibly attached to amino acids in histone tails Methyl groups attached to histone tails can promoted condensation of the chromatin and the attachment of a phosphate group neXt to a methylated amino acid can have the opposite effect The histone code hypothesis proposes that speci c combinations of modi cations help determine the chromatin con guration which in turn in uences transcription 3 DNA METHYLATION Certain enzymes can methylate certain bases in the DNA itself Usually genes that are heavily methylated are not eXpressed Removal of methyl groups can turn on some genes A dual mechanism that involves both methylation of the DNA and deacetylation of histones can repress certain transcription In some species DNA methylation seems to be essential for the longterm inactivation of genes that occurs during normal cell differentiation in the embryo De cient DNA methylation due to lack of methylating enzyme leads to abnormal embryonic development in mice and Arabidopsis Once methylated genes usually remain that way through successive cell divisions in a given individual eg genomic imprinting in mammals 4 EPIGENIC INHERITANCE Mutations in the DNA are permanent while changes in the chromatin can be reversed Chromatin modi cation already discussed may be passed along to future generations of cells Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenic inheritance Enzymes that modify chromatin structure are integral parts of the eukaryotic cell s machinery for regulating transcription REGULATION OF TRANSCRIPTION INITIATION Transcription in both eukaryotic and prokaryotic cells requires an initiation site and a promoter to which RNA polymerase binds l ORGANIZATION OF A TYPICAL EUKARYOTIC GENE A cluster of proteins called the transcription initiation complex assembles on the promoter sequence at the upstream end of the gene Then RNA polymerase II proceeds to transcribe the gene synthesizing the premRNA Associated with most eukaryotic genes are multiple control elements segments of noncoding DNA that help regulate transcription by binding certain proteins These control elements and the proteins they bind are critical to the precise regulation of gene expression seen in different cell types 2 THE ROLES OF TRANCRIPTION FACTORS RNA polymerase needs the assistance of proteins called transcription factors in order to initiate transcription Some transcription factors are essential for the transcription of all proteincoding genes they are often called general transcription factors Only a few general transcription factors bind to DNA sequences such the TATA box within the promoter Others bind to proteins including each other and RNA polymerase II Proteintoprotein interactions are crucial to the initiation of eukaryotic transcription The interaction of general transcription factors and RNA polymerase II with a promoter usually leads to only a low rate of initiation and production of few RNA transcripts High levels of transcription of particular genes at the appropriate time and place depend on the interaction of control elements with another set of proteins which ca be thought of a speci c transcription factors 3 ENHANCERS AND SPECIFIC TRANSCRIPTION FACTORS Proximal control elements are located closer to the promoter More distant control elements are called enhancers Enhancers are DNA sequences that increase the rate of transcription An enhancer can regulate a gene thousands of base pairs away They may be located upstream or downstream of the promoters they control or even within an intron A given gene may have multiple enhancers each active at a different time or in a different cell type or location in the organism Each enhancer is associated with only one gene and no other Activator proteins bind to distal control elements grouped as an enhancer in the DNA A DNAbending protein brings the bound activators closer to the promoter The activators bind to certain mediator proteins and general transcription factors helping them for an active transcription initiation compleX on the promoter These multiple proteinprotein interactions help assemble and position the initiation compleX on the promoter Researchers have identi ed two common structural elements in a large number of activator proteins a DNAbinding domain and one or more activation domains Repressors can bind to the DNAbinding site of the activator proteins or to proteins that allow the activators to bind to DNA Some activators and repressors act indirectly on transcription by affecting chromatin structure Some activators recruit proteins that acetylate histones near the promoters of speci c genes thus promoting transcription Others recruit proteins that deacetylate histones leading to reduced transcription this is called silencing 4 COMBINATORIAL CONTROL OF GENE ACTIVATION The different nucleotide sequences found in control elements are small when considering the large number of genes that have to be regulated On the average each enhancer is composed of about ten control elements each of which can bind only one or two speci c transcription factors A particular combination of control elements will be able to activate transcription only when the appropriate activator proteins are preset which may occur at a precise time during development or in a particular cell type 5 COORDINATELY CONTROLLED GENES IN EUKARYOTES In bacteria genes are often clustered together into an operon which is regulated by a single promoter and transcribed into a single mRNA molecule These types of operons have not been found in eukaryotic cells In eukaryotic cells some genes are clustered but each gene has its own promoter and is individually transcribed The coordinate regulation of these clustered genes is thought to involve changes in chromatin structure that make the entire group of genes either available or unavailable for transcription In nematodes some genes share an promoter but the RNA transcript is processed into separate mRNAs CoeXpressed eukaryotic genes are most commonly found scattered in different chromosomes The coordinate gene expression seems to depend on the association of a speci c combination of control elements with every gene of a dispersed group Copies of the activators that recognize the control elements bind to them promoting simultaneous transcription of the genes no matter where they are in the genome Coordinate control of dispersed gene often occurs in response to chemical signals from outside the cells eg steroid hormones MECHANISMS OF POST TRANSCRIPTIONAL REGULATION Prokaryotic mRNA is transcribed in a form that can be translated immediately Eukaryotic mRNA requires further modi cations before it can be translated 1 Multiple splicing patterns of exons alternative RNA splicing can yield different proteins The splicing pattern depends on the tissue 2 Degradation of mRNA is due to enzymatic action that begins by shortening the polyA tail Enzymes degrade bacterial mRNA within a few minutes of their synthesis In multicellular eukaryotes m RNA can survive for hours days or weeks Increasing the life of mRNA molecules allows more proteins to be formed 3 The initiation of translation of some mRNAs can be blocked by regulatory proteins that bind to speci c sequences or structures within the untranslated region a the 5 end preventing the attachment of ribosomes Translation of all the mRNAs in a cell may be regulated simultaneously It usually involves the activation or inactivation of one or more of the protein factors required to initiate translation eg the activation of translation initiation factors right after fertilization of the egg 4 Protein processing and degradation Often eukaryotic polypeptides must be processed in order to yield functional proteins Regulation may occur at any step involved in modifying or transporting a protein Regulatory proteins are commonly activated or deactivated by the reversible addition of phosphate groups or by the addition of sugars to proteins destined to the surface of animal cells To mark a protein for destruction the cell attaches molecules of a small protein called ubiquitin to the protein Giant protein complexes called proteasomes then recognize the ubiquitintagged protein and degrade them NONCODING RNA PLAY lVlULTIPLE ROLES IN CONTROLLING GENE EXPRESSION About 15 of the human genome codes for proteins Most of the rest of the DNA was thought until recently to contain no meaningful genetic information A major part of the genome may be transcribed into nonproteincoding RNA also called noncoding RNA Regulation by noncoding RNAs occurs at two points in the pathway of gene expression mRNA translation and chromatin con guration MICRORNAS AND SMALL INTERFERING RNAS Micro RNA miRNA binds to complementary strands of mRNA RNA precursor folds back into itself forming a short double stranded hairpin structure held together by H Ai1ners1zyme cuts each hairpin from the primary miRNA transcript A second enzyme called dicer trims the loop and the single stranded ends from the hairpin On strand of the double RNA is degraded The other strand then forms a compleX with one or more proteins The miRNA in the compleX can bind to any target mRNA that contains at least siX bases of complementary sequence The miRNA compleX either degrades the target mRNA or blocks its translation It is estimated that up to one third of human genes are regulated by miRNA Small interfering RNA is similar in size and function as miRNA It can turn off genes The difference between the two is based on the nature of the precursor molecule for each siRNA is formed from a much longer doublestranded RNA CHROMATIN REMODELING AND SILENCING OF TRANSCRIPTION BY SMALL RNA Small RNAs appear to be crucial in the formation of 39 39 39 at the of 39 An RNA transcript produced from DNA in the centromeric region of the chromosome is copied into doublestranded RNA by an enzyme and then processed into siRNAs These siRNAs associated with proteins move to the centromeric region and recruit enzymes that modify the chromatin turning it into a heterochromatin Chromatin remodeling blocks the eXpression of large regions of the chromosome Noncoding RNA can regulate gene eXpression at multiple steps DIFFERENTIAL GENE EXPRESSION LEAD TO THE DIFFERENT CELL TYPES IN MULTICELLULAR ORGANISMS Embryonic development involves cell division cell differentiation and morphogenesis During embryonic development cells increase in number Cells also become specialized in structure and function This is called differentiation As cells differentiate they become arranged in tissues and organs The physical processes that give an organism its shape constitute morphogenesis GENETIC PROGRAM OF EMBRYONIC DEVELOPMENT Development or ontogeny is an orderly predictable sequence of events beginning with fertilization and ending with death It includes fertilization embryogenesis birth infancy childhood adolescence adulthood senescence and deat Morphogenesis is the process by which an animal takes shape and the differentiated cells end up in the appropriate locations During differentiation cells become specialized in structure and function CYTOPLASMIC DETERMINANTS AND INDUCTIVE SIGNALS Genes that are eXpressed in cells control differentiation of cells Development requires the timely differentiation of many kinds of cells in speci c locations In many animals the uneven quot quot 39 of p39 39 39 39 in the f quot39 39 egg leads to regional differences in the early embryo Maternal substances in the cytoplasm of the egg 0 RNAs and proteins encoded by the mother s genome o Substances in the cytoplasm are not evenly distributed 0 Distribution of substances in uences the development of the future embryo Interaction among embryonic cells brings about changes in gene eXpression which in turn bring about the differentiation of specialized cell types This is called induction The environment of the cell 0 Embryonic cells send signals to other embryonic cells including contact with cell surface molecules 0 Signal molecules send cells down a speci c path of differentiation SEQUENTIAL REGULATION OF GENE EXPRESSION DURING CELLULAR DIFFERENTIATION Determination refers to the events that lead to the observable differentiation of a cell At the end of determination the cell is irreversibly committed to its nal fate and it is said to be determined Observable cell differentiation is marked by the expression of genes for tissuespeci c proteins Differentiated cells are specialists at making these tissuespeci c proteins Liver cells make albumins lens cells make crystallins muscle cells make actin and myosin The rst evidence of differentiation is the appearance of mRNAs for these proteins These proteins are found only in a speci c cells type and give the cells its characteristic structure and function The appearance of mRNA for these proteins is the rst evidence of differentiation Beginning with the rst mitotic division the cells set on a path to specialization At a certain moment the cells become irreversibly committed to its nal fate This is called determination Determination is the outcome of molecular changes in the cell caused by the expression of genes for tissue speci c proteins On the molecular level different sets of genes are sequentially expressed in a regulated manner as new cells arise from division of their precursors PATTERN FORMATION SETTING THE BODY PLAN Before morphogenesis can shape an animal or plant the organism s body plan 7 its overall three dimensional arrangement 7 must be established Pattern formation is the development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places The axes of an animal are established very early head and tail right and left front and back The molecular cues that control pattern formation collectively called positional information tell a cell its location relative to the body axes and to neighboring cells and determine how the cell and its progeny will respond to future molecular signals Cytoplasmic determinants and inductive signals are the substances that initially establish the axes of the animal body s GENETIC STUDIES ON DROSOPHILA Key developmental events in the life cycle ofDrosophila on page 370 371 1 GENETIC ANALYSIS OF EARLY DEVELOPMENT SCIENTIFIC INQUIRY Edward Lewis was the rst to use a genetic approach to study embryonic development in Drosophila Antennae legs and wings develop on the appropriate segments The anatomical identity of the segments is set by master regulatory genes called homeotic genes Homeotic genes specify what kind of appendages and other structures are going to develop in each segment Mutations of the homeotic genes cause the development of appendages on the wrong segments eg legs on the head Embryonic lethals are mutations with phenotypes causing death at the embryonic stage or larval stage All these genes encode transcription factors These regulatory proteins control the expression of the genes responsible for speci c anatomical structures Homeotic proteins activate genes specifying the proteins that actually build the y structures The homeotic genes of Drosophila directly correspond to similar gene complexes in animals all the way up to man Many of the proteins found on y pattern formation have been found to have close counterparts throughout the animal kingdom The homeotic genes here called quotHOMquot genes in Drosophila are clustered close to each other in the DNA and they set a ground plan for embryonic development in the y Vertebrates also contain homeotic HOX genes Here we nd four clusters or complexes of homeotic genes These genes are closely related to the insect genes their order in the DNA is the same and their action during embryonal development follows the same order in time and space in the y Thus the effects on the embryonic headto tail axis of these HOX genes largely follow the principles which Lewis39 set up for the y It is actually possible to transfer a HOX gene from man to the embryo of a fruit y where it is can perform some of the functions that the corresponding Drosophila gene normally executes The location of our shoulders and hips on the vertebral column for example may be controlled by speci c homeotic genes Source httn39 nnhelnri e quot 39 39 199 quot39 1 39 html 39 199 39 39 html 2 AXIS ESTABLISHMENT Genetic analysis of Drosophila reveals how genes control development Cytoplasmic determinants are already present in the unfertilized egg and are coded by genes of the mother called maternal effect genes Mutations in these maternal effect genes result in defective phenotypes in the offspring or the fertilized egg fails to develop properly regardless of the offspring s own genome Maternal effects genes are also called eggpolarity genes because they control the orientation polarity of the egg Messenger RNA produced by the mother and concentrated at one end of the egg act as pattern setter for the anterioriposterior end of the embryo bicoid gene bcd another group of maternal effect genes establishes the dorsalventral axis An embryo Whose mother has mutant bcd gene lacks the front half of its body and has posterior structures at both ends The bcd mRNA is concentrated at the anterior end of the mature egg After fertilization the mRNA is translated into protein The bicoid protein diffuses from the anterior end toward the posterior resulting in a gradient of protein Within the early embryo The bad is a maternal morphogen a substance that establishes the embryo s axes Morphogens are the products of eggpolarity genes They are transcription factors proteins that regulate the activity transcription of some of the embryo s own genes The morphogen gradient hypothesis was rst proposed a century ago gradients of substances called morphogens establish an embryo s axes and other features of its form Segmentation pattern Gradients of these morphogens bring about regional differences in the expression of segmentation genes the genes of the embryo that direct the actual formation of segments after the embryo s major axes are de ned A cascade of gene activations sets up the segmentation pattern in Drosophila There are three sets of segmentation genes These sets of genes are activated sequentially and provide the positional information for increasingly ne details of the animal body plan They produce transcription factors that directly activate the next set of genes in the hierarchical scheme of pattern formation Gap genes map out the basic subdivisions along the anteriorposterior axis of the embryo Mutations in the map genes cause an embryo to miss a given segment Pair rule genes are the second set of segmentation genes to act They subdivide these broad bands into pairs of segments Mutations in the pairrule genes causes to have half the normal number of segments because every other segment fails to develop The segment polarity genes set the anteriorposterior axis of each segment Mutations in the segment polarity genes cause each segment to have a mirror image repetition of one side on the other side Genes in each set not only activate the next set of genes but also maintain their own expression in most cases Other segmentation genes operate indirectly l l 39 the L 39 39 of the 391 39 factors in various ways eg components of cellsignaling pathways signal molecules and receptor molecules The ultimate difference between cells is transcriptional regulation the turning on and off of certain genes TYPES OF GENES ASSOCIATED WITH CANCER Genes for growth factors their receptors and the intracellular molecules of signaling pathways can mutate and lead to cancer 1 ONCOGENES AND PROTOONCOGENES Protooncogenes code for proteins that stimulate normal cell growth and division Oncogenes are cancercausing genes The products of protooncogenes and tumorsuppressor genes control cell division A DNA change that makes a protooncogene or its protein product excessively active converts it to an oncogene which may promote excessive cell division and cancer Cancer cells often contain chromosomes that have broken and rejoined incorrectly translocating fragments from one chromosome to another The protooncogene may end up near an especially active promoter its transcription may increase making it an oncogene 2 TUMORSUPPRESSOR CELLS A tumorsuppressor gene encodes a protein that inhibits abnormal cell division A mutation in such a gene that reduces the activity of its protein product may also lead to excessive cell division and possibly cancer Tumor suppressor proteins are involved in Repair DNA and help prevent accumulation of cancer causing mutations Control adhesion of cells to each other or to the extracellular matrix normal adhesion is absent in cancer cells Cellsignaling proteins that inhibit the cell cycle 3 INTERFERENCE WITH NORMAL CELLSIGNALING PATHWAYS Many protooncogenes and tumorsuppressor genes encode components of growthstimulating and growthinhibiting signaling pathways respectively A hyperactive version of a protein in a stimulatory pathway such as RAS a G protein functions as an oncogene protein A defective version of a protein in an inhibitory pathway such as p53 a transcription activator fail to function as a tumor suppressor 4 THE MULTISTEP MODEL OF CANCER DEVELOPMENT Normal cells are converted to cancer cells by the accumulation of mutations affecting protooncogenes and tumorsuppressor genes More than one mutation is needed to produce all the changes characteristics of a cancer cell This may eXplain why the longer we live the more likely we are to develop cancer About a half dozen changes must occur at the DNA level for a cell to become fully cancerous These mutations usually include one active oncogene and the mutation or loss of several tumor suppressor genes 0 Tumorsuppressor alleles are usually recessive o Oncogenes are dominant In many malignant tumors the gene for telomerase is activated This enzyme reverses the shortening of chromosome ends during DNA replication Production of telomerase in cancer cells removes a natural limit on the number of times the cells can ivi e 5 INHERITED PREDISPOSITION AND OTHER FACTORS COTRIBUTING TO CANCER Individuals who inherit a mutant oncogene or tumorsuppressor allele have an increased risk of developing cancer Certain viruses promote cancer by integration of viral DNA into a cell s genome Chapter17 FROM GENE TO PROTEIN How is the message of a gene translated by cells into a specific trait such as brown hair or type A blood In 1909 Archibald Garrod was the first to suggest that gene dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell Biochemists accumulate evidence that showed that cells degrade organic molecules in a series of steps each catalyzed by an enzyme 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 Researchers realized that not all proteins are enzymes They shifted from one gene one enzyme to one gene one protein In the mid 1950 s it became evident that the genetic information in DNA contains the code for all the proteins needed by the cell Most of the basic work was done with bacterial DNA The information encoded in DNA is used to specify the sequences of amino acids in proteins BASIC PRINCIPLES OF TRANSCRIPTION AND TRANSLATION Genes provide the instructions for making specific proteins RNA or ribonucleic acid serves as an intermediary between DNA and protein DNA provides the template for the sequence of RNA nucleotides in the same way it provides the template for a new DNA strand DNA 4 RNA 4 protein Transcription is the synthesis of RNA under the direction of DNA This takes place in the nucleus of the cell 0 The immediate product of transcription is the premessenger RNA and RNA processing yields the finished mRNA 0 The initial product of transcription including the RNA sections that are not translated into proteins is called a primary transcript Translation is the synthesis of the polypeptide under the instructions of the mRNA This occurs in the cytoplasm of the cell with the help of ribosomes GENETIC CODE The genetic code is the sequence of nucleotides in DNA that specify for amino acids Triplets of nucleotides code for or specify all 20 the amino acids that make proteins During transcription the gene determines the base sequence along the length of the RNA For each gene only one of the two DNA strands is transcribed For each gene one DNA strand functions as a template for transcription the synthesis of a complementary RNA molecule This molecule of RNA is called a messenger RNA or mRNA The RNA molecule is complementary to the DNA template rather than identical The RNA bases are assembled according the base pairing rules except that U pairs with A in the DNA and ribose replaces deoxyribose The RNA strand is synthesized like a new DNA strand during replication in an antiparallel direction 0 3 ACC5 in DNA 4 5 UGG3 in RNA The genetic code is defined at the mRNA level 0 Marshall Niremberg and his colleagues were the first to decipher a codon in the early 1960s They used the multiple copies of the triplet UUU uracil to make a polyuracil This strand of repetitious UUU synthesizes a polypeptide containing only the amino acid phenylalanine The base triplets are called codons The genetic code is made of continuous nonoverlapping triplets of bases This is called the reading frame There are 64 codons 61 code for amino acids and 3 serve as stop signals The start codon is AUG which also specifies the amino acid methionine o Codons are read in a 5394 direction along the mRNA e g 5 AUG3 a The code is universal all organisms use the same code e g CCG is translated in ALL organisms as the AA proline AUG stands for the amino acid methionine Met and also functions as the start signal for ribosomes to begin translating the mRNA at that point Three of the 64 codons function as stop signals marking the end of a genetic message Exception to the universality of the genetic code are found in a few protozoans like Paramecium vary in theirtranslation system and in some mitochondria and chloroplasts that transcribe and translate their small DNA The genetic code is redundant with the exception of methionine and tryptophan more than one codon designates each amino acid e g GAA and GAG code for glutamic acid Glu A code never codes for more than one amino acid there is no ambiguity 0 Genetic information is encoded as a sequence of nonoverlapping base triplets or codons each of which is translated into a specific amino acid during protein synthesis There are a few exceptions to the universality of the genetic code 0 Some unicellular eukaryotes and organelle genes 0 Some prokaryotes have can translate stop codons into AA not found in most organisms TRANSCRIPTION Transcription is the synthesis of RNA from a DNA template Transcription means copying RNA is a polymer of nucleotides RNA DNA Single stranded Double stranded helix Ribose Deoxyribose Uracil Thymine Three kinds of RNA are transcribed from DNA ribosomal RNA rRNA transfer RNA tRNA and messenger RNA mRNA Messenger RNA or mRNA carries the specific information for making proteins 1 Initiation o Transcription begins when an RNA polymerase II binds to a DNA sequence known as the promoter 0 The promoter extends several dozen nucleotide pairs from the start point towards the 539 end of the DNA strand 0 The promoter determines which DNA strand is to be transcribed and is the point of attachment of the RNA polymerase II o The DNA unwinds and the enzyme initiates RNA synthesis at the start point on the template strand 0 The sequence that signals the end of transcription is called the terminator o The stretch of DNA that is transcribed is called a transcription unit 2 Elongation RNA polymerase II binding and initiation of transcription ln prokaryotes RNA polymerase II binds directly to the promoter There are several kinds of RNA polymerases in eukaryotes each with a specialized function RNA polymerases are complexes each complex containing about 12 subunits or polypeptides ln eukaryotes a group of at least seven proteins called transcription factors contribute to the binding of RNA polymerase II to the promoter These enzymes are present in all cells and have many similarities to the DNA polymerases Eukaryotic promoters include a TATA box a nucleotide sequence containing TATA about 25 nucleotides upstream from the transcriptional start point The TATA boxes are given as they occur in the nontranscribing DNA strand A transcription factor that recognizes the TATA box must bind to the DNA before RNA polymerase II can attach Additional transcription factors become attached to the promoter and form together with RNA polymerase II the transcription initiation complex Once the transcription initiation complex is in place the double helix unwinds and synthesis begins at the start point As the RNA polymerase II moves the DNA continues to unwind exposing 10 to 20 bases at a time for pairing with RNA nucleotides In the wake of the advancing RNA synthesis the double helix reforms and the RNA molecule just synthesized peels away from the DNA template strand The RNA polymerase II uses nucleotides with three phosphate groups as substrates They remove two phosphates as the subunits are covalently linked to the 3 end of the growing RNA molecule These reactions are strongly exergonic Messenger RNA contains the base sequence that codes for proteins RNA synthesis does not require a primer but other proteins are needed The first nucleotide at the 5 end retains its threephosphate group This is called the 539 cap and has a protective function The last nucleotide to be incorporated has an exposed 3 OH group The termination of transcription is controlled by a specific base sequence Different genes may have different promoter sequences upstream from the proteincoding sequence Once the RNA polymerase II has recognized the promoter it unwinds the helix and begins transcription The DNA is read in a 3 to5 direction Upstream means toward the 5 end Downstream means toward the 3 end Example Nontranscribed DNA strand 5 A T G A C T 3 Transcribed DNA strand template 3 T A C T G A 5 RNA P P P 5 A U G A C U 3 OH 999999999 Transcription progresses at a rate of about 60 nucleotides per second Messenger RNA contains additional base sequences that do not code for proteins The leader sequence at its 5 end contains recognition signals for ribosome binding which allow the ribosomes to be properly positioned to translate the message 9quot Termination At the end of the coding sequence there is a special termination or stop codon UAA UGA or UAG are termination codons When the RNA polymerase II transcribes a stop codon transcription stops Leader sequence 9 coding sequence 9 termination codon The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit Termination of Transcription In prokaryotes transcription proceeds through a terminator sequence in the DNA The transcribed terminator in the RNA functions as the termination signal causing the polymerase to detach from the DNA and release the transcript n eukaryotes the premRNA is cleaved from the growing RNA chain while RNA polymerase II continues to transcribe the DNA The RNA polymerase II continues for hundreds of nucleotides past the termination signal The termination signal in the DNA codes for what is called the polyadenylation signal AAUAAA in premRNA molecule About 10 to 35 nucleotides past the AAUAAA the RNA is cut fee from the polymerase enzyme The polymerase detaches from the DNA by a mechanism that is not understood EUKARYOTIC CELLS MODIFY RNA AFTER TRANSCRIPTION Alteration of mRNA ends The newly synthesized premRNA is modified before it goes to the cytoplasm The 539 end is capped off with a modified form of a guanine nucleotide unusual nucleotide 7 methyl guanylate 1 It helps to protect the mRNA from degradation by hydrolytic enzymes 2 The 539 cap signal the place of attachment of the mRNA to the ribosomes The 339 end is capped with polyA tail consisting of some 50 to 250 adenine nucleotides The function of the polyA tail is similar to that of the 539 cap protective and attachment to ribosomes The 339 also facilitates the export of the mRNA from the nucleus to the cytoplasm Example of a capped premRNA G P P P UTR start codon 5 A U G A C U UTRAAUAAA 3 AAAAAAAAA There are sections of the RNA besides the polyA tail and the 5 cap that will not be translated These regions at the 5 and 3 ends are called UTR for untranslated regions Translation modifications noncoding and coding sequences Most eukaryotic genes and their RNA transcripts have long noncoding sequences of nucleotides These noncoding stretches of nucleotides do get translated The noncoding regions are called introns intervening sequences The coding regions are called exons expressing sequences Genes may have multiple introns and exons The entire gene is transcribed and it contains both introns and exons This is called precursor mRNA or premRNA lntrons must be removed and the exons spliced together forthe mRNA to become functional 1 The premRNA combines with small nuclear ribonucleoproteins snRNPs and other proteins to form a molecular complex called a spliceosome 2 Within the spliceosome snRNPs base pairs with nucleotides at the ends of the intron 3 The RNA transcript is cut and the intron is released and exons are spliced together Then the spliceosome is released Ribozymes RNA is capable of catalyzing some reactions In a few cases the splicing of exons occurs without the assistance of enzymes the intron catalyzes its own excision Ribozymes are catalytic RNA molecules Functions of introns Some introns seem to control gene activity Some genes give rise to two or more polypeptides by alternative RNA splicing Different segments of the RNA can be treated as introns or exons Some proteins have structural and functional sections that perform two functions e g catalytic and attachment to the membrane These areas are called domains Domains are coded for by different exons lntrons increase the probability of crossing over between genes without interfering with coding sequences It increases the chances of recombination between two alleles and of crossing over between homologous chromosomes New and potentially useful proteins could arise in this way This reshuffling of exons may contribute to the evolution of protein diversity PROTEIN SYNTHESIS Translation is protein synthesis During translation the mRNA is decoded The fourbase mRNA is converted into a 20amino acid polymer Transfer RNA Transfer RNA is the decoding molecule in the translation process Transfer RNA is made in the nucleus and travel to the cytoplasm where it takes an amino acid and delivers it to the ribosome to be incorporated into a protein The tRNA is used repeatedly in both prokaryotes and eukaryotes Each tRNA is specific for one amino acid The cell keeps a stock of amino acids in its cytoplasm At one end of the tRNA molecule there is a threebase anticodon which is complementary to a threebase codon in the mRNA At the other end of the tRNA an amino acid is attached The AA becomes attached to the tRNA before becoming incorporated into a polypeptide The carboxyl group of an AA becomes attached to the 3 end of a tRNA The amino group is left free to participate in peptide bond formation Specialized regions of the tRNA Anticodon complementary to a mRNA codon Site for amino acid binding 0 O 0 Site for ribosomal recognition 0 Site for the aminoacyltRNA synthetase recognition Wobble hypothesis There are 61 codons but the usual number of tRNA is 45 Some cells have only 40 different tRNA to pair with 61 codons The third base 5 end on the anticodon is sometimes capable of forming hydrogen bonds with more than one kind of nucleotide of a mRNA codon 3 end Some tRNA can recognize up to three different codons AminoacyltRNA synthetases A tRNA that binds to an mRNA codon specifying a particular amino acid must carry only that amino acid to the ribosome There has to be a correct match between the tRNA and the amino acid Amino acids are attached to their respective tRNA by specific enzymes called aminoacyltRNA synthetases The aminoacyltRNA synthetase is specific for each amino acid There are 20 of these nzymes The binding of the tRNA and amino acid is an endergonic process that occurs at the expense of ATP The result is an activated amino acid called aminoacyl tRNA The resulting complex is called aminoacyltRNAs bind to the messenger RNA coding sequence Ribosomes Ribosomes have a catalytic function and a structural function to hold the mRNA the aminoacyltRNA and the growing polypeptide chain Ribosomes couple the tRNAs to their proper codons on the mRNA and facilitate the formation of peptide bond between amino acids Each ribosome is made of a large and small subunit each subunit contains one molecule of ribosomal RNA and large amount of proteins In eukaryotes the subunits are made in the nucleolus Each ribosome has three depressions called the A and P sites after the word aminoacyltRNA site and peptidyltRNA site and the E site for exit site The tRNA holding the polypeptide chain occupies the P site The tRNA bringing the next amino acid to be incorporated into the chain occupies the A site The ribosome holds the tRNA and the mRNA close together and positions the new amino acid for addition to the carboxyl end of the growing polypeptide Then the formation of the peptide bond is catalyzed and formed Before translation begins the ribosomal subunits are dissociated Protein synthesis is divided into three stages initiation elongation and termination Initiation Initiation begins when the mRNA a tRNA with the first amino acid of the peptide and the two subunits of the rRNA come together The sequence of nucleotides at either end of the mRNA molecule helps to bind the molecule to the ribosomal subunit In all organisms the codon forthe initiation of protein synthesis is AUG which codes for the amino acid methionine This is called the initiation tRNA 1 Messenger RNA binds to the small ribosomal subunit The subunit binds attaches to the 539 end of the mRNA l The initiation tRNA binds to a specific codon called the start codon o the tRNA anticodon UAC binds to the start codon AUG This tRNA carries the amino acid methionine 3 The large ribosomal subunit then binds to the small one creating a functional ribosome Proteins called initiation factors bring all these components together 4 When the initiation process is completed the initiator rRNA sits in the P site of the ribosome and the vacant A site is ready for the next aminoacyl tRNA The synthesis of peptides is initiated at its amino end which is called the Nterminus The other end is called the Cterminus C for the carboxyl end Elongation The initiatortRNA is bound to the P site of the ribosome The A site is unoccupied Amino acids are added one by one to the polypeptide chain 1 Codon recognition The anticodon of an incoming aminoacyltRNA carrying an amino acid binds to the codon of the mRNA in the A site The bonds are hydrogen bonds 0 Elongation factors bring the tRNA to the A site 0 This reaction requires energy which is provided by 2 molecules of GTP guanosine triphosphate 2 Peptide bond formation The polypeptide separates from the tRNA to which it was bound in the P site and attaches by a peptide bond to the amino acid carried by the tRNA in the A site 0 The amino group of the AA at the A site is aligned with the carboxyl of the AA in the P site o The ribosome catalyzes the reaction The enzyme is called peptidyl transferase a component the large ribosomal subunit 0 RNA catalysts are called ribozymes 3 Translocation The tRNA at the P site now leaves the ribosome and ribosome translocates moves the tRNA in the A site carrying the growing peptide chain to the P site The mRNA moves with it o The codon and anticodon remain bonded and the mRNA and tRNA move as a unit 0 The next mRNA codon is brought in to the A site 0 Energy is supplied by GTP o Translocation occurs in a 5 to3 direction of the mRNA Termination 1 Translocation is repeated many times until a stop codon reaches the ribosome A site 2 The codons UAA UAG and UGA do not code for amino acids but signal to stop translation 3 A protein called release factor binds directly to the stop codon in the A site 4 The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain 5 This reaction hydrolyzes the complete polypeptide from the tRNA that is in the P site freeing the polypeptide from the tRNA that is in the P site 6 The ribosomes dissociate into the two subunits which can then be used to form a new ribosome A single ribosome can make an average size polypeptide in less than a minute Polyribosomes A polyribosome or polysome is a complex of one mRNA and many ribosomes Once the ribosome moves past the initiation code a second ribosome can attach to the mRNA and start its own translation of a new polypeptide A mRNA is generally translates simultaneously by several ribosomes Polyribosomes occur in both prokaryotic and eukaryotic cells POSTTRANSCRIPTION MODIFICATIONS IN EUKARYOTES The basic features of transcription and translation are the same in prokaryotes and eukaryotes Eukaryotic mRNA molecules undergo specific posttranscriptional modification and processing before they become competent for transport and translation After synthesis the polypeptide begins to fold forming a functional protein a three dimensional protein with its secondary and tertiary structure A gene determines the primary structure The primary structure in turn determines conformation Certain amino acids may become modified by the attachment of sugars lipids phosphate groups or other molecules Some amino acids may be removed from the leading end of the polypeptide In some cases the polypeptide may be cut in two or more pieces or two polypeptides that have been synthesized separately may be joined to form the quaternary structure of a functional protein Signal mechanism for targeting proteins to the ER Free ribosomes are suspended in the cytosol and make proteins that dissolve and function in the cytosol Bound ribosomes are attached to the cytosol side of the ER membrane They make proteins of the endomembrane system nuclear envelope ER Golgi apparatus lysosomes vacuoles and plasma membrane and protein that are secreted by the cell Polypeptide synthesis begins in the cytosol A sequence called signal peptide made of about 20 amino acids near the leading amino end of the polypeptide is recognized by a proteinRNA complex called the signalrecognition particle SRP as it emerges from the ribosome The SRP binds to a receptor protein in the ER membrane The receptor is part of a protein complex that has a pore and a signalcleaving enzyme The SRP leaves and the polypeptide resumes growing emerging into the cisternal space of the ER through the protein pore The signal peptide is removed by an enzyme The finished polypeptide is released into the cistern or remains partially embedded in the ER membrane if it is destined to that structure Types of RNA in a eukaryotic cell 1 Messenger RNA tRNA and rRNA 2 Primarytranscript or premRNA direct product of transcription contains introns and exons 9 Small nuclear RNA snRNA part of the spliceosomes the complexes of protein and RNA that splice premRNA in the nucleus 4 SRP RNA part of the signal recognition of polypeptides destined to the ER 5 Small interfering RNA siRNA and microRNA miRNA have been recently discovered and are involved in regulating which genes get expressed 6 Small nucleolar RNA snoRNA aid s in processing prerRNA transcripts in the nucleolus MUTATIONS A gene is a functional unit Mutations are disruptions on the structure of a chromosome or changes in a single base pair of nucleotides Point mutations are chemical changes in one base pair of a gene Basepair substitution in the DNA results in a different base pairthat will be transcribed into an altered mRNA Basepair substitutions could be 0 Missense mutations result in the replacement of one amino acid for another this replacement may or make not make quotsensequot 0 Nonsense mutations convert an amino acid specifying codon into a termination codon Insertions and deletions are additions or losses of nucleotide pairs in a gene In a frameshift mutation one ortwo nucleotides are inserted or deleted from the DNA As a result the codons downstream of the insertion specify an entirely new sequence of amino acids Mutations can be produced by errors in DNA replication by physical agents radiation or by chemicals called mutagens 0 Base analogues a re similarto normal DNA bases but pair incorrectly during DNA replication Chemicals that insert themselves in the DNA and distort the double helix Chemicals that change the structure of the bases and their chemical properties What is a gene A region of the DNA encoding a polypeptide or an RNA molecule as their final products SUMMARY OF THE CHARACTERISTICS OF THE GENETIC CODE 0 Messenger RNA consists of only four bases A G C and U forming chains of various lengths and sequences 0 mRNA codon that specifies a given AA is a triplet of three nucleotides I 1 0 Each codon is translated in a continuous three at a time o The code is nonoverlapping o The codon sequence complements an anticodon sequence in the adapter tRNA 0 The code is universal All living organisms share the codons that specify the same AA 0 The same codon does not specify two or more AA There are no ambiguities 0 Except for methionine and tryptophan all AA are designated by more than one codon 64 codons specify 20 AA and chain termination o Degeneracy in the third codon position Wobble hypothesis the third nucleotide of the tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon Chapters WATER AND THE FITNESS OF THE ENVIRONMENT All organisms are made mostly of water and live in an environment dominated by water Water is the biological medium on Earth Life on Earth began in water and evolved there for 3 billion years before spreading onto land Modern life remains tied to water Living cells are 70 95 water Water covers about 3 of the Earth In nature water naturally exists in all three physical states of matter gas liquid and solid THE EFFECTS OF WATER39S POLARITY Water unique behavior depends on its structure and the interaction of its molecules Polarity of water molecules results in hydrogen bonding The water molecule is shaped like a V Oxygen is more electronegative than hydrogen and pulls the electron pair closerto itself The hydrogens acquire a partial positive charge Water is a polar molecule Water molecules attract each other the slightly positive hydrogen 6 of one molecule is attracted to the slightly negative oxygen 639 of a nearby molecule FOUR EMERGENT PROPERTIES OF WATER 1 Organisms depend on the cohesion of water molecules Hydrogen bonds hold the water molecules together This is called cohesion Hydrogen bonds are about 120 the strength of covalent bonds when water is its liquid state This bonds form break and reform frequently Because at any given time most water molecules are bonded to its neighboring molecules water is a more structure liquid than most other liquids Water can also cling to other substances that are polar or partially polar This is called adhesion Cohesion and adhesion are responsible for the movement of water up the plant Hydrogen bonds makes waterto be Cohesive water molecules are attracted to each other Adhesive water molecules are attracted to molecules on the surface of objects The attraction is due to the formation of hydrogen bonds Capillary action and surface tension is the result of these attractive forces 0 O O 0 Surface tension is a measure of the difficulty in breaking or stretching the surface of a liquid The energy of motion is kinetic energy Atoms and molecules are always moving they have kinetic energy Heat is a measure of the total quantity of kinetic energy due to molecular motion in a body of matter A form of energy representing aggregated internal energy of motions of atoms and molecules in a body Mass is an important consideration when talking about heat the greaterthe mass the greater the heat 2 Moderation of temperature Water moderates air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler Heat is the energy that can be transferred between objects of different temperature It is the total amount of kinetic energy due to molecular motion in a substance that its bulk is not moving Temperature is a measurement of the average kinetic energy of a substance Science uses the Celsius scale to measure temperature 0 Water has a high specific heat 0 1 calorie raises 1 g of water 1 C 0 1 cal 4184 joules 1 J 0239 cal Specific heat is refers to the amount of energy required to raise the temperature of 1 gram of a substance 1 C The specific heat of water is 1 callgraml1 C Compare to most other substances water has an unusually high specific heat Because of its high specific heat water will change its temperature less when absorbing or losing heat absurbs ur re eases neat Heak of vaporixa on s amuunt uf Energythat rnds1 be absumed by1 g uf hqmd water at mm m enange m 1 g uf vvatervapur gas at 1 C 539 7D eamg ur mad1g 4mm Jmm we a gmu rurvvatertu Wyeth Energy Tne mu ecmesthat remam have a uvver average Wyeth Energy They are Bunker ann 12m 1am 2am zonn zann aznn Heatabsorbed Tbe magvam bn me Wen sbbwsme umake b1 heat bw kg mmen as n passes 1mm me at Van c m s1eam at tempevamves abuve mu c aneusme Empevamve dube same A Rwse m tempevatuve as me absuvbs heal a A sb mm thealu usmn sawe c Fusemempevamveasudmdwa evabsbvbsbeat D Wale buds and absuvbs alem beamwapbnzabbn 225mm E Steam absuvbs heat and thus mueases ds tempevatuve Tbe abuve san examme maheamb mme One cbmd vevevsem pvucess and man acnnlmu curve The al nbmbnsmsucb curves ndmambe pbase cbanees nng HWWWQh senern en zaHeaVLatent ntrn 3 Ice insulates bodies ofwaker Water Expands when dneezes Water ebntraets as n cums dbvvn m NC Attmstemperature Water 5 denses t As water continues to cool from 4 C to 0 C it expands and becomes less dense than liquid water Heat of fusion 797 calg or 3335 Jg o 1 thermochemical calorie 4184 J When water begins to freeze the molecules do not have enough kinetic energy to break hydrogen bonds As the crystalline lattice forms each water molecule forms a maximum of 4 hydrogen bonds which keeps water molecules further apart than they would be in the liquid state Because of the large space this arrangement takes ice has fewer water molecules than in equal volume of liquid water Expansion of water contributes to the fitness of the environment for life 1 Prevents deep bodies of water from freezing solid from the bottom up 2 Since ice is less dense it forms on the surface firs As water freezes it releases heat to the water below and insulates it 3 Makes transitions between seasons less abrupt As water freezes hydrogen bonds form releasing heat As ice melts hydrogen bonds break absorbing heat 4 Water is a solvent A solution is a homogeneous mixture of two substances 0 The dissolving agent is the solvent 0 The substance that is dissolved is the solute An aqueous solution is one in which water is the solvent In a solution the solute is broken down to the ionic or molecular level If an ionic crystal is dissolved positive and negative ions go into solution The negative oxygen region of the polar water molecules is attracted to the positive ion The positive hydrogen region of the polar water molecules is attracted to the negative ion The surrounding water molecules shield the positive and negative ions from one another The water molecules form a hydration shel Water molecules can form hydrogen bonds with other particles Hydrophilic substances interact readily with water A hydrophilic substance may or may not dissolve eg cotton is made of cellulose which is hydrophilic but cotton does not dissolve Water adheres to the cellulose molecules Hydrophobic substances repel water Hydrophobic substances are nonionic and nonpolar Some cell components are so large that they remain in suspension although they are hydrophilic These substances form colloids a stable suspension of fine solid particles in a liquid MOLES One mole of a substance contains 602 x1023 atoms or molecules 602 x 1023 is called Avogadro39s number The mass of one mole of a substance is equivalent to the number of amu of the atom or molecule of that substance Example What is the mass of one mole of water H20 has 18 daltons 16 daltons of oxygen and 2 daltons of hydrogen 1 mole of H20 contains 602 x1023 molecules and has a mass of 18 grams One mole of a substance has the same number of molecules than one mole of another substance Both have 602 x 1023 molecules but their mass will be different Molarity is the number of moles of solute per liter of solution 1 M 1 mole1 liter of solution Summary Four emergent properties of water 1 Cohesion 2 Moderation of Temperature 3 Insulation of bodies of water by floating ice 4 Solvent of life DISSOCIATION OF WATER Water can dissociate into H and OH39 This leads to acidic or basic conditions that affect living organisms 2H20 320 OH39 The dissociation of water is reversible The hydrogen ion does not exist by itself as a single proton but it becomes attached to a water molecule to form a hydronium ion H30 The anion OH39 is called a hydroxide ion At 25 C the concentration of hydronium and hydroxide ions is 10397 M molar That means that only one water molecule in 554 million dissociates ACIDS AND BASES Acids are proton H donors bases are proton acceptors Acids tend to increase the number of protons in a solution Bases reduce the hydrogen ion concentration by accepting protons H NH3 H mu Many bases dissociate to produce hydroxide ions HO39 which tend to accept H NaOH a Na OH39 The hydroxide ions then combine with hydrogen ions to form water and the hydrogen ion concentration becomes reduced Strong acids and bases dissociate completely in water Weak acids and bases dissociate partially These substances reversibly release and reaccept hydrogen and hydroxide ions H2C03 is a weak acid that releases H and HCO3 In any solution the product of H and OH39 is constant at 1039 H OH39 103914 In a neutral solution H 10397 and OH39 107 Therefore 107 1071 103914 If enough acid is then added to the solution to increase the H concentration up to 10395 M then the concentration of OH39 will decline to 109 The final product of both concentrations is still 1039 The pH scale measures the concentration of hydrogen ions protons in a solution 7 is neutral Below 7 is acid and above 7 is basic or alkaline It is based on the negative logarithm base 10 of the hydrogen ion concentration in a neutral solution log10397 7 7 Notice that as pH declines the concentration of H increases A pH of 10 has an acid concentration of 103910 and a hydroxide concentration of 104 This is a basic or alkaline solution The pH for acid solutions is below 7 and for basic solutions above 7 Buffers Buffers are combinations of H donor and H acceptor that form weak acids or bases When the H are in excess they accept them and release H when they have been depleted Buffer solutions resist changes in pH when acids or bases are added They minimize changes in the concentrations of H and OH39 ngfers help maintain the pH of body fluids within the narrow range necessary for life usually pH Organisms have many weak acids and weak bases that maintain an essential buffering capacity and avoid pH extremes Salts are compounds in which the hydrogen atom of an acid is replaced by some other cation Reactions of acids with bases form salts Electrolytes are salts acids and bases that conduct electricity when in solution Nonelectrolytes do not conduct water when in solution eg sugar alcohols Acid precipitation Acid precipitation is rain snow or fog with a pH below 56 It has been recorded to reach a pH of 15 in West Virginia It often results from a reaction in the air between water vapor and sulfur oxides and nitrogen oxides produced by the combustion of fossil fuels Acid precipitation can change the solubility of minerals in the soil e g Ca and Mg are washed away More information about acid rain httpwwwepagovacidrain httpwww 39 quot 39 39 nhn7 html Summary of chapter 3 I L httpjWWW Na mm A sion 1 Polarity of water molecules and hydrogen bonding 2 Four emergent properties of water 3 Cohesion adhesion 4 Moderation of ambient temperature 0 specific heat o heatofvaporization o evaporative cooling 5 Insulation of bodies of water by floating ice 6 Water as a solvent 0 importance to life 0 hydrophilic and hydrophobic substances 7 Dissociation of water 0 Hydrogen ion Hydroxide ion Acids and bases pH scale Buffers 8 Acid rain what is acid rain PRINCIPLES OF BIOLOGY September 10 2004 Test 1 Name Ch 14 Multiple choice 40 points 1 Which is the best description of the science of biology a The study of life b The study of rocks c The study of humans d The study of biodiversity e The study of the way humans interact with their environment 2 A maple leaf is at which level in the hierarchical organization of life a Tissue c Organ e Organelle b Population d Organism 3 Which of the following is the main source of energy for producers such as plants a Light c Carbon dioxide d Minerals b Heat d Chemicals 4 What name is given to the process by which plants convert the energy of light to chemical energy Feedback mechanism c Evolution e Photosynthesis Homeostasis d Cellular respiration 575 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 svslwwm 6 A rose bush is classified into Domain and Kingdom wepve 999579 wepvee wepvee wepvee wnovww 69m 057 2 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 39 A resul A question c 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 A B and 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 Y Hydrogen bonds Nonpolar covalent bonds Polar covalent bonds In a single molecule of water the two hydrogen atoms are bonded to a single oxygen atom b 9 lonic bonds Van derWaals interactions D 4 What determines the cohesiveness of water molecules Hydrophobic interactions High specific heat Covalent bonds Hydrogen bonds lonic bonds 3999579quot A 5 Electrons exist only at fixed levels of potential energy However if an atom absorbs sufficient energy a possible result is that a An electron may move to an electron shell farther out from the nucleus b The atom may become a radioactive isotope c An electron may move to an electron shell closerto the nucleus d The atom would become a positively charged ion e The atom would become a negatively charged ion 16 Organic chemistry is the branch of chemistry that studies a biochemical processes b physiological processes c oxygen compounds d carbon compounds e none of the above A 7 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 different atomic number One more neutron One more proton One more electron A different charge 051057 8 Which of these statements is true of all anions The atom has more electrons than protons The atom has more protons than electrons The atom has fewer protons than does a neutral atom of the same element The atom has more neutrons than protons The net charge is 1 999579quot 9 There is unity in the diversity of life This unity is evident in The universal genetic code Similar metabolic pathways or cell functions Similar cell structure A and B only are correct A B and C are correct 0905794 N O Weak temporary attractions between atoms and molecules are called Polar bonds c Nonpolar bonds e Covalent bonds lonic bonds d Van der Waals interactions 5339 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 9 Water can cling to molecules of other substances that are polar or partially polar This is called 10 The energy of motion is called 11 The amount of energy required to raise the temperature of 1gram of a substance 1 C is called 12 A is a homogeneous mixture of two substances The dissolving agent is called the The substance that is dissolved is the 13 39 repel water 14 Solutions resist changes in pH when acids or bases are added are called 15 NH3 H lt gt NH4 therefore ammonia is a because it accepts a 16 The thermometer is used to measure the energy of the molecules 17 Molecules made of only carbon and hydrogen atoms are called 18 Name given to isomers that are mirror images of each other Usually one form is biologically active and the other is not 19 Amines are organic compounds having the functional group called lll True or false 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 Chapter7 MEMBRANE STRUCTURE AND FUNCTION The plasma membrane separates the cell living from the outside world nonliving and defines the cell as a distinct entity The plasma membrane is selectively permeable it shows selective permeability o It allows some substances to pass through and prevents others from passing through The main functions of the plasma membranes The main functions of the plasma membranes 1 The plasma membrane helps maintain a lifesupporting internal environment by regulating the passage of materials in and out of the cell 2 Plasma membranes receive information that permits the cells to sense changes in the environment and respond to them 3 Communication between cells takes place through the plasma membrane 4 Biochemical reactions occur on their surface MEMBRANE STRUCTURE Biological membranes are made of lipids and proteins forming a double layer or bilayer There are also carbohydrates The most common lipids are phospholipids Phospholipids are am phipathic molecules they have a hydrophobic and a hydrophilic region Membrane proteins also have hydrophobic and hydrophilic regions History 1895 Charles Overton hypothesized that membranes were made of lipids 1917 Irving Langmuir made artificial membranes by adding phospholipids dissolved in benzene 1925 E Gorter and F Grendel proposed that membranes were a phospholipid bilayer two molecules thick 1935 Hugh Davson and James Danielli proposed a sandwich model a phospholipid bilayer between two layers of globular proteins In 195039s electron microscopy seem to support the DavsonDanielli model and by By 196039s the DavsonDanielli had become widely accepted as the structure of the plasma membrane By the end of 196039s questions about all cell membranes being identical began to arise 0 Differences in thickness and appearance between plasma and mitochondrial membranes 0 Differences in phospholipid and protein content and type 0 Position of proteins and their hydrophobic parts 1972 S J Singer and G Nicolson proposed that the proteins are embedded in the bilayer with only the hydrophilic region exposed to the liquid medium This is called the fluid mosaic model Membranes are fluid Membrane proteins are mostly mobile and do not remain static in one location Phospholipids move laterally in a membrane They may flipflop from the outer layer to the inner layer or viceversa This is a rare event Unsaturated hydrocarbon tails have kinks that prevent phospholips from packing together This helps the fluidity of the membrane Proteins are much larger than phospholipids and some drift along the membrane The movement of some proteins is very directed probably due to connections to the cytoskeleton Many proteins are however anchored to the cytoskeleton and remain fixed Cholesterol molecules are part of the plasma membrane At high temperatures 37 C in humans it interferes with phospholipid drifting and membrane fluidity At low temperatures interferes with the packing of phospholipids and the freezing of the membrane It lowers the solidification point of the membrane 0 Changes in the fluidity of the membrane will affect its function MEMBRANE PROTEINS Proteins are embedded in a matrix of phospholipids The proteins determine most of the specific functions of the membranes INTEGRAL PROTEINS are embedded in the bilayer with the hydrophilic side exposed to the aqueous environment and the hydrophobic side inside the bilayer TRANSMEMBRANE PROTEINS are integral proteins that pass through the bilayer from side to side Transmembrane proteins may function as channels or pores through which small ions and watersoluble molecules can pass others act as carriers that bind to a substance and move it through the membrane PERIPHERAL PROTEINS are not embedded in the bilayer but are usually bonded to integral proteins by noncovalent interactions The outer and inner side of the plasma membrane has a different arrangement of proteins Proteins are arranged asymmetrically and each side of the membrane has different characteristics On the cytoplasmic side of the plasma membrane some proteins are held in place by the cytoskeleton On the exterior side of the plasma membrane some proteins are attached to fibers of the extracellular matrix The two layers of the membrane may differ in phospholipid composition and the proteins have a directional orientation in the membrane The membrane also has carbohydrates which are restricted to the exterior surface Some carbohydrates are attached to membrane proteins The asymmetrical distribution of phospholipids proteins and carbohydrates is determined as the membrane is being built by the endoplasmic reticulum Function of the membrane proteins Transport across the membrane Enzymatic activity Signal transduction lntercellularjoining Cellcell recognition Attachment to the cytoskeleton and ECM o SnPP N Role of carbohydrates in cell to cell recognition Cells have the ability to distinguish one type of neighboring cell from another This is important during embryonic development when the sorting out of cells into tissues occur It is the basis for the rejection of foreign cells by the immune system Carbohydrates are important in cellcell recognition Membrane carbohydrates are usually shortchained saccharides called oligosaccharides consisting of less than 15 sugar units Membrane carbohydrates on the external side of the plasma membrane vary from species to species among individuals of the same species and from one cell type to another in the same individual Some are covalently bonded to phospholipids forming glycolipids most are bonded to proteins forming glycoproteins o Membrane proteins and lipids are synthesized in the ER Carbohydrates are added here to make glycoproteins and glycolipids The carbohydrate portion may then be modified The glycoproteins are transported from the ER to the Golgi complex in small vesicles and released in the cis portion of the Golgi facing the same way as in the ER the side that was facing the lumen in the ER also faces the lumen in the Golgi apparatus Enzymes in the Golgi complex lumen further modify the carbohydrate branch of the glycoproteins and incorporated into secretory vesicles The secretory vesicles move to the plasma membrane and fuse with it exposing the carbohydrate chain of the glycoprotein to the outside of the cell Membrane proteins are involved in the transport of materials in and out of the cell act as enzymes receive stimuli and transmit information function in cell recognition and link cells together Oligosaccharides on the external side of the membrane vary from species to species individual to individual and from cell to cell They act as markers than distinguish one cell from another In signal transduction a receptor protein converts an extracellular signal into an intracellular signal that causes some change in the cell using a series of molecules that relay information from one to another TRAFFIC ACROSS THE MEMBRANE Cells are bathed in and extracellular fluid called the interstitial fluid that is derived from the lood This fluid contains thousands of ingredients like amino acids carbohydrates fatty acids vitamins hormones neurotransmitters salts and waste products The cell must extract from this soup the exact amounts of the substances it needs at specific time and reject the rest The membrane has the ability to regulate traffic across its phospholipid bilayer Selective permeability Selectively permeable membranes allow the passage of some substances and prevent others from passing through Biological membranes are usually permeable to small molecules and lipidsoluble substance 0 Water gases 02 molecules 39 39 N2 C02 CO small polar molecules glycerol larger nonpolar 39 39 39 39 like 39 39 39 and some fats alcohol I Biological membranes are impermeable to and use proteins to transport the following types of molecules 0 lons amino acids and sugars e g glucose The hydrophobic center of the bilayer prevents the direct passage of ions and polar molecules which are hydrophilic through the membrane TRANSPORT PROTEINS Hydrophilic substances enter the cell through transport proteins thus avoiding contact with the hydrophobic core of the membrane These transport proteins span the membrane 1 Channel proteins are like tunnels used by ions and polar molecules to enter the cell eg aquaporins 2 Carrier proteins change shape in a way that pushes the hydrophilic substance to the other side of the membrane Both transport proteins are specific for the substance that is to be transported PASSIVE TRANSPORT Passive transport is the diffusion ofa substance through a biological membrane and it does not require energy o It depends on the concentration gradient 0 The concentration gradient represents the potential energy TRANSPORT MECHANISMS Diffusion and active transport require energy 0 Concentration gradient provides the energy for diffusion also called passive transport 0 ATP requires the energy for active transport 1 Simple diffusion Diffusion is movement of molecules down the concentration gradient from the area of high concentration to the area of low concentration using the kinetic energy of the molecules This results in even scattering of molecules throughout the environment The greater the difference in concentration between two areas of the environment the faster diffusion will occur Dialysis is the diffusion of a substance through a membrane Osmosis is the diffusion of water a solvent through a membrane from the region of high water concentration to the region of low water concentration 0 Osmotic pressure of a solution is the tendency of water to move from the area of high concentration to the area of low concentration Much of the traffic across the membrane occurs by diffusion This is called passive transport The concentration gradient represents potential energy and drives diffusion Diffusion is unaffected by the presence of other substances A solution with high solute concentration eg salt has in effect low water concentration and high osmotic pressure lsotonic solutions have the same osmotic pressure Eg the cell has the same solute concentration as its environment Hypertonic solutions have higher solute concentration than other solution Eg the environment has greater concentration than the cell so the environment is hypertonic to the cell The cell loses water and becomes plasmolyzed plasmolysis Hypotonic solutions have lower solute concentration than other solution Eg the environment has lower concentration than the cell so the environment is hypotonic to the cell The cell swells Turgor pressure is the pressure caused by the cell of plants against the cell wall when the cell swells with water Cells lacking walls are isotonic to their environment or have adaptations for osmoregulation the control of water balance 0 In a hypertonic solution these cells lose water shrivel and die They become plasmolyzed o In a hypotonic solution these cells will take in water swell and eventually burst Cells with walls are those of plants fungi and some protists In a hypertonic solution these cells will also become plasmolyzed In a hypotonic solution the cells will swell until they begin to exert pressure against the cell wall The cell wall will exert a backpressure that will counteract the pressure of the swollen cell At this point the volume will not increase any more and water will leave the cell in the same amount as it enters The cell is turgid very firm and has reached a point of equilibrium 2 Carriermediated transport Specialized integral membrane proteins move ions or molecules across the membrane A Facilitated diffusion Uses the concentration gradient as the energy source Concentration gradient must be maintained Some integral proteins provide a corridorthrough which ions and molecules can pass through the membrane following the concentration gradient Molecule binds to integral protein It cannot work against the gradient Transmembrane protein changes shape and open a channel through the membrane Shape change allows the release of the molecule into the cytoplasm gated channels Transmembrane protein reverts to its original shape when the molecule is released A stimulus electrical chemical is necessary for the gated channels to open 111 Carriermediated active transport 0 The cell spends energy from ATP to move ions or molecules across the membrane against the concentration gradient lons bind to the transmembrane protein the pump Phosphate group is transferred from ATP to the transport protein Transport protein undergoes a conformational change and ions are released to the other side of the membrane Membrane potential All cells have voltages across the membrane Voltage is electrical potential energy due to the separation of charges positive from negative 0 The cytoplasm of the cell tends to be negative due to an unequal distribution of charges on both sides of the membrane The voltage across the membrane is called the membrane potential This membrane potential favors the passage of cations to the inside of the cell and of anions out of the cell 0 An electrochemical gradient is created when ions are stored against the concentration gradient 0 Two forces drive the diffusion of ions across a membrane the ion s concentration gradient and the electrical force that attracts to the side of the membrane with the opposite charge Learn the example of the sodiumpotassium pump on page 135 A transport protein that generates a membrane potential is called an electrogenic pump Proton pumps are electrogenic pumps 3 Cotransport ln cotransport and ATPpowered system transports ions or molecules and indirectly powers the movement of other solutes by maintaining a concentration gradient 0 ATP is used to create a gradient of ions or molecules 0 When these ions or molecules move back to the lower concentration area they carry with it the molecules of a solute against the solute concentration gradient 0 ATP energy is used indirectly o Gradient energy is used directly 4 Exocytosis The cell releases metabolic products to the outside through the fusion of a vesicle with the plasma membrane 5 Endocytosis In endocytosis materials are taken into the cell by engulfing the material with a portion of the plasma membrane and forming a vesicle or vacuole that is released inside the cell Types of endocytosis A Phagocytosis A particle or cell is engulfed and a vacuole is formed B Pinocytosis Dissolved materials are taken into the cell by forming a vesicle around the droplets of fluid trapped in folds of the plasma membrane C Receptormediated endocytosis Specific molecules called ligands bind with receptor molecules in depressions of the plasma membrane called coated pits The pits are coated with a layer of protein called clathrin The receptor molecule bind with the ligand then forms a coated vesicle that is released to the inside of the cell Coating detaches from the vesicle leaving an uncoated vesicle The vesicle is now called an endosome Endosome divides into a vesicle that returns receptors to plasma membrane and a second vesicle that fuses with a lysosome The contents are digested and returned to the cytosol httn39lr ellhin utmh 39 quot39 39 I 439 hfmjtlateo39of Example Cholesterol is removed from the blood in the form LDL lowdensity lipoprotein by receptor mediated endocytosis lfthe receptors are defective LDL remains in the blood leading to atherosclerosis the formation of plaque on the blood vessel inner surface Here is some additional information about LDL and HDL and their removal from the blood stream What are the differences in the structures and effects of quotgoodquot and quotbadquot cholesterol Provided by Andrea Ladd postdoctoral fellow Ba ylor College of Medicine Houston former HHMI predoctoral fellow Cholesterol is a waxy fatty substance found in all the cells of your body Like other lipids such as fats cholesterol is not soluble in water or in blood which is largely made of water To be transported therefore cholesterol needs to be helped by special carrier molecules called lipoproteins These carriers are what are being referred to when you hear about quotgoodquot and quotbadquot cholesterol Highdensity lipoprotein or HDL is the good kind and the bad kind is low density lipoprotein or LDL High concentrations of HDL have been shown to lower your risk of heart attack It is thought that HDL carries cholesterol away from the arteries and to the liver which breaks it down On the other hand lots of LDL cholesterol in your bloodstream leads to the deposition of cholesterol in your arteries Together with other substances the cholesterol then forms artery clogging plaques that in the arteries feeding your brain or heart can lead to stroke or heart attack The major component of both HDL and LDL cholesterol is a protein called apolipoprotein l t associates with cholesterol by forming a protein shell around the insoluble cholesterol creating a discoid or spherical particle The structures of the HDL and LDLcholesterol molecules themselves are essentially the same but HDL cholesterol has a higher density of apolipoprotein relative to the amount of associated cholesterol than LDL does hence the nomenclature There are however different forms of apolipoprotein and the exact composition of different cholesterolcontaining particles can differ The apolipoproteins on the surfaces of the particles interact with receptors on the surfaces of other cells leading to uptake in the liver for HDL particles or deposition in blood vessels for LDL particles httQllwwwhhmiorglcgibinaskascientistlhighlightplkwampfileanswers2Fmolecular 2Fans 012html this link does not work anymore 2004 Howard Hughes Medical Institu te httpusers rrn 39 39 quot ma quot quotBiooqua n n I l html alternate link IL 4 4 4 14 Highdensity quot HDL in the 39 39 g 39from body tissues and transporting it to the liver for excretion or recycling Increased levels of HDL have been 39 39with a 39 39risk 0 39 39 a primary cause of cardiovascular disease Nascent HDL particles are discoidal consisting of a phosphatidylcholine bila yer and a protein shell which shields the hydrophobic lipid tails from the aqueous environment As it circulates in the body HDL collects cholesterol which is then stored in the lipid bilayer Increased efficiency is achieved though the quot quot of the le ithin 39 39 39acyl L CA T enzyme that converts the amphipathic cholesterol stored in the bila yer into hydrophobic cholesterol esters which collect among the lipid tails This induces a transformation of the HDL disk to a spherical form in which a hydrophobic core of cholesterol esters is shielded by a combination of lipid and protein At this stage cholesterol collection ceases and the mature HDL particle is recognized by the liver httpllwwwksuiucedulResearchagoa1l James C Phillips Willy Wriggers Zhigang Li Ana Jonas and Klaus Schulten Predicting the structure of apolipoprotein Al in reconstituted highdensity lipoprotein disks Biophysical Journal 7323372346 1997


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