Biology 105: Biology of Salmon Exam 1
Elongation of the RNA Strand
As RNA polymerase moves along the DNA it untwists the double helix→enzyme adds nucleotides t the 3' end of the growing RNA molecule The new RNA molecule peels way from its DNA template→DNA double helix re-forms
assymetric crossing over
Asymmetric crossing over can lead to gene duplication and gene deletion. Gene duplication is one of the important mechanisms in evolution
External factors that can influence cell division:
Cells fail to divide if an essential nutrient is lacking in the culture medium
chemical modificaitons to histone proteins and DNA
Certain chemical modifications to the histone proteins and to the DNA of chromatin can influence both chromatin structure and gene expression o →the effects of these modifications are catalyzed by specific enzymes
chromosome translocation
Chromosome translocation results from crossing over between non-homologous chromosomes, which produces totally new linkage groups.
Building on the Work of Others
Cooperation is facilitated when scientists use the same organism
differences between organisms and nucleotide sequences
Differences between orgnaisms reflect difference between their nulcuetoides sequences
chrosomsoal structure mutaitons- duplication
Duplication = doubling of chromosome segments. Tandem, reverse tandem, and tandem terminal duplications are three types of chromosome duplications. Duplications also result in un-paired loops visible cytologically. (e.g., Fig. 21.2)
Gastrulation overview
During gastrulation, the cells engulf the yolk sac, and outer tissue (ectoderm) differentiates from middle tissue (mesoderm) and inner tissue (endoderm).
Mitosis and Chromosomes
During mitosis the chromosome becomes condensed→they can be distinguished from one another by their size, the positions of their centromeres, and the pattern of colored band produced by certain chromatic-binding stains
HOM-C or HOX genes
Each of the HOM-C, or Hox, genes contains a "homeobox" region of 180 base pairs that codes for a sequence of 60 amino acids that comprises the "homoedomain" region of the protein, which will then bind with DNA elsewhere as transcription factors or enhancer proteins Homeosis ("like condition") complex, or HOM-C genes in Drosophila melanogaster; these genes code for proteins that are transcription factors --> they bind to DNA to activate transcription.
sexually reproducing species characteristics diploid and haploid number
Each sexually reproducing species has a characteristic diploid and haploid number o The fruit fly Drosphila has a diploid number of 2n of 8 and a haploid number of n of 4
haploid and diploid cells and mitosis
Either haploid or diploid cells can divide by mitosis depending on the type of life cycle o Only diploid cells can undergo meiosis because haploid cells have only a single set of chromosomes that cannot be further reduced
Eukaryotes gene expression increase or decrease
Eukaryotes: the are o gene expression can be strongly increased or decreased by the binding of specific transcription factors, either activators or presressors, to the control elements of enhancers
what protects the genes of linear eukaryotic chromosomes from being erorides away during successive rounds of DNA replication?
Eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends
Chapter 1
Evolution, the Themes of Biology, and Scientific Inquiry
Exception
Exceptions include the UTRS of the exons at the ends of the RNA-make up a part of the mRNA but are not translated into proteins
E. coli
" a bacterium that normally live in the intestines of mammals and is a model organism for molecular biologists" o The T2 phages could quickly turn an E.coli cell into a T2-prducing factory that release many copies of new phages when the cell ruptured
checkpoint
" a control point in the cell cycle where stop and go-ahead signlas can regulate the cycle. Three important checkpoints are found in the g1, g2 and M ohases
Nuclear matrix
" a framework of fibers extending through the interior of the nucleus"
Clone
" a group of genetically identical individuals"
frameshift mutation
" a mutation in which the reading frame of the genetic message is altered" o occurs whenever the number nucleotides inserted or deleted is not a multiple of three
nonsense mutation
" a point mutation in which changes a codon for an amino acid into a stop codon" o causes translation to be terminated prematurely→the polypeptide will be shorted than the polypeptide encoded by the normal gene o usually all lead to nonfunctional proteins
RNA splicing
" a processing in the eukaryotic nucleus in which there is the removal of large portions of the RNA molecule that is initially synthesized" o Cuts down from 27,000 nucleotide pair to 1,2000 nucleotides
euchromatin
" a type of chromatin that is loosely coiled and is often times termed true chromatin"
recombinant chromosomes
" individual chromosomes that vary genes (DNA) derived from two different parents"
Antiparallel
" running in the opposite directions"
Promoter
" the DNA sequence where RNA polymerase attaches and initiates transcription"
Ribozymes
"RNA molecules that function as enzymes" • In some organism: RNA splicing can occur without proteins or even additional RNA molecules o The intro RNA functions as a ribozyme can catalyze its own excision
replication fork
"a Y-shaped region where the parental strands of DNA are being unwound"
transformation
"a change in genotype and phenotype due to the assimilation of external DNA by a cell"
TATA box
"a crucial promoter DNA sequence in forming the initiation complex at a eukaryotic promoter"
Trombone model
"a model in which two DNA polymerase molecules (one at each template strand )"reel in" the parental DNA and extrude newly made daughter DNA molecules"
transfer RNA (tRNA
"a molecule that transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome" o a cell keeps its cytoplasm stocked with all 20 amino acids o the ribosome adds each amino acid brought to it by tRNA to the growing end of a polypeptide chain
mutagens
"a number of physical and chemical agents that interact with DNA in ways that cause mutations o ex: x-rays and other forms of high-energy radiation pose hazard to the genetic material of organisms o magnetic radiation includes ultraviolet light which can cause disruptive thymine dimers in DNA
histone acetylation
"a process in which promotes transcription by opening up the chromatin structure and adding methyl groups in order to condense chromatin and reduce transcription"
growth factor
"a protein released by certain cells that stimulates other cells to divide" o Differwnt cell types respond specifically todifferent frowth factors
release factor
"a protein shaped like an aminoacyl tRNA that binds to the stop codon in the A site and causes the addition of a water molecule instead of an amino acid to the polypepetide chain" o breaks the bond between the complete polypeptide and the tRNA in the P site→releases the polypeptide through the exit tunnel of the ribosomes large subunit
Asexual reproduction
"a single individual is the sole parent and passes copies of all its genes to its offspring without the fusion of gametes" o Ex: single-celled eukaryotic organisms can reproduce asexually by mitotic cell division o Some multicellular organism also capable of reproducing asexually b/c the cells of the offspring derived by mitosis in the parent the child s sually genetically identical to its parent -->An individual that reproduces asexually gives rise to a clone
mRNA
"a type of RNA molecule that carries a genetic message from the DNA to the protein-synthesizing machinery of the cell"
heterochromatin
"a type of interphase chromatin in which is highly condensed similar to that seen in a metapahse chromatin"
Genes
"account for family resemblances" o Program specific traits that emerge as we develop from fertilized eggs into adults o Written in the language of DNA o Inherited information is passed on in the form of each genes specific sequence of DNA nucleotides o Most genes program cells to synthesize specific enzymes and other proteins→produces an organisms inherited traits
insertions or deletions mutations
"additions or losses of nucleotides pairs in a gene" o have a disastrous effect on the resulting protein more often than substitutions do o may alter the reading frame of the genetic message (the triplet grouping of nucleotides on the mRNA that is read during translations)
Autosomes
"all chromosomes that are not sex chromosomes"
Dispersive model
"all four strands of DNA following replication have a mixture of old and new DNA"
DNA ligase
"an enzyme that joins the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand"
Diploid cell
"any cell with two chromosome sets; had a diploid number of chromosomes, abbreviated 2n"
• transcription factories
"areas on which chromosomes cross over and are specialize for a common function"
meiosis
"cell division that reduces the number of sets of chromosomes from two to one in the gametes, counterbalancing the doubling that occurs at fertilization" o As a result each human sperm and egg is haploid (n=23) o Fertilization restores the diploid condition by combining two hapliad sets of chromosomes
point mutations
"changes in a single nucleotide pair of a gene" o gamete or in a cell that gives rise to gamete: may be transmitted to offspring and to future generations o if the mutation has an adverse effect on the phenotype of a person the mutant condition is referred to as a genetic disorder or hereditary disease o the change of a single nucleotide in the DNA's template strand can lead to the production of abnormal proteins
binary fission
"division in half refers to the his process and to the asexual reproduction of single-celled eukaryotes" o the process in eukaryotes involves mitosis but in prokaryotes does not
Telomeres
"do not contain genes, the DNA typically consist of multiple repetitions of one short nucleotide sequences and have two protective functions" 1. specific protein associated with telomeric DNA prevent the staggered ends of the daughter molecules from activating the cells systems for monitoring DNA damage 2. telomeric DNA acts as a kind of buffer zone that provides some protection against the organisms genes shortening →telomeres do not prevent the erosion of genes near the ends of chromosomes; they merely postpone it • telomeres become shorter during every round of replication o it has been proposed that shortening of telomeres is somehow connected to the aging process of certain tissues and even to aging of the organism as a whole
independent assortment
"each pair sorting it maternal and paternal homologs into daughter cells independently of every other pair"
aminoacyl-tRNA synthetases
"enzymes that carry out the correct matching up of tRNA and amino acid" o there are 20 different synthetases→each able to bind to all the different tRNA that code for its particular amino acid o →synthetase catalyzes the covalent attachment of the amino acid to its tRNa in a process driven by the hydrolysis of ATP o →the results aminoacyl tRNA is released from the enzyme and s then available to deliver its amino acid to a growing polypeptide chain on a ribosome
helicase
"enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands"
Mutations
"genetic variations"
• Enhancers
"groupings of distant vital control elements" • A given gene may have multiple enhancers each active at a different time or in a different cell type or location in the organism o Each enhancer however is generally associated with only that gene and no other
Specific trasnscription factors
"high levels of transcription of particular genes at the appropriate times and place depend on the interaction of control elements with another set of proteins"
Malignant tumor
"includes cells whose geetic and cellular changes enable them to spread to new tissues and impair the function of one or more organs" o These cells also considered "transformed cells" o These ces may ave unsual numbers of crhomsoms o Their metabolism may be altered and they may cease to function in a constructive way -->An individual with a malignant tumor is said to have cancer
Epigenetic inheritance
"inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself"
virus
"little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein." o To produce more viruses a virus must infect a cell and take over the cells metabolic machinery
Distal control elements
"located far from the promoter"
MPF
"maturation-promoting factor" or "M-phase-promoting factor" b/c it triggers the cells passage into the M phase, past the G2 checkpint"
ribosome
"molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains"
mismatch repair
"other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors" o researchers spotlighted the importance of such enzymes when they found that a hereditary defect in one of them is associated with a form of colon cancer
Watson and Crick Paper:
"our model of DNA is in effect a pair of templates, each of which is complementary to the other...prior to duplication the hydrogen bonds are broken, and the two chains unwind and separate. Each cahin then acts as a template for the formation on to itself of a new companion chain, so that eventually we shall have two pairs of chains...the sequence of the pairs of bases will have been duplicated exactly"
Variation
"refers to diversity in gene frequencies." o can refer to differences between individuals or to differences between populations. o Mutation is the ultimate source of genetic variation, but mechanisms such as sexual reproduction and genetic drift contribute to it as well.
bound ribosomes
"ribosomes that are attached to the cytosolic side of the endoplasmic reticulum or to the nuclear envelop" o make ortens of the endomembrane system (the nuclear envelope, ER, Golgi apparatus, lysomes, vacuoles, and plasma membrane as well as proteins sevrteted from the cell, such as insulin)
free ribosomes
"ribosomes that are suspended in the cytosol and most synthesize proteins that stay in the cytosol and function there"
poly A-tail
"the addition of 50-250 more adenine nucelotides to the 3' end of an mRNA molecule
Exons
"the coding segments of nucleic acids
Allele
"the different versions of genes on a homolog"
primase
"the enzyme that synthesizes primer" o primase starts a complementary RNA chain from a single RNA nucleotide adding more RNA nucleotides one at a time using the parental DNA strand as a template o the complete primer is based paired to the template strand
Gene expression
"the expression of different genes by cells with the same genome"
Life Cycle
"the generation-to-generation sequence of stages in the reproductive history of an organism, from conception to its production of its own offspring"
primer
"the initial nucleotide chain that is a short stretch of RNA"
codons
"the mRNA nucleotide triplets" o customarily written in the 5'→3' direction o can also be used for the DNA nucleotide triplets along the non template strand
Alternation of Generations
"the means of reproduction by plants and some species of algae in which the sporophyte generation produces a gametophyte as its offspring and the gametophyte generation produces the next sporophyte generation and so on an so forth"
double helix
"the model of DNA in which DNA is made up of two anti-parralel strands"
Poisitional information
"the molecular cues that control pattern formation"
natural selection
"the natural environment slects for the propogation of cetain traits among naturally occurring variant traits in the population"
introns
"the noncoding segments of nucleic acid that lie between coding regions"
start point
"the nucleotide where RNA synthesis actually begins • RNA polymerase ends in a precise location and orientation on the promoter→determining where transcription starts + which of the two strands of DNA helix is used as the template
DNA replication
"the process in which DNA is replicated
RNA processing
"the process in which enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways before the genetic message is dispatched to the cytoplasm" o Both ends of the primary transcript are altered o In most cases certain interior sections of the RNA molecule are cut out and the remaining parts spliced together o →these modification produce an mRNA molecules ready for translation
Silencing
"the process in which some receptors recruit proteins that remove acetyl groups from histones and thus reduce transcription"
nucleotide-pair substitution
"the replacement of one nucleotide and its partner with another pair of nucleotides:
zygote
"the resulting fertilized egg" • The zygote is diploid b/c it contains two haploid sets of chromosomes • As a human develops into a sexually mature adult mitosis of the zygote and its descendent cells generates all the somatic cells of the body • Both chromosome sets in the zygote and all the genes they carry are passed with precision to the somatic cells
Karyotype
"the resulting ordered display of chromosome pairs by size, largest to smallest"
Terminator
"the same a promoter but for bacteria"
Genetics
"the scientific study of hereditary and hereditary variation"
Okazaki segments
"the segments of the lagging strand in which are synthesized discontinuously" whereas only one primer is required of the leading strand each Okazaki fragment on the lagging strand must be primed separately
transcription
"the synthesis of RNA using info in the DNA" o the info is simply transcribed or rewritten from DNA to RNA o DNA strands can serve as a template for assembling a complementary sequence of RNA nucleotides o For a protein-coding gene the resulting RNA molecule is a faithful transcript of the genes protein building instruction
translation
"the synthesis of a polypeptide suing the info in the mRNA" o there is a change in language→the cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide o the site of translate are ribosomes
Hereditary
"the transmission of traits from one generation to the next o Sons and daughters are not identical copies or either parent o There is also variation
Transcription initiation complex
"the whole complex of transcription factors and RNA polymerase II bound to the promoter"
fertilization
"this union of gametes, accumulating l in fusion of their nuclei"
General transcription factors
"transcription factors that are essential for the transcription of all protein coding genes" • A few general transcription factors being to a DNA sequence such as the TATA box within the promoter but most bind to proteins including other transription factors and RNA polymerase II
bacteriophages or phages
"viruses that infect bacteria"
Semiconservative model
"when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand"
sister chromatid cohesion
(Sister chromatids are two copies of one chromosome, closely associated along their lengths) "the association of two sister chromatids along their lengths" the sister chromatids make up one duplicated chromosome
Meiosis Diagram
(look at word document)
small interfering RNA's
(siRNAs0: "similar in size and unction to miRNAS both can associated with the same proteins producing similar results" o is siRNA precursor RNA molecules are injected into a cell the cells machinery can process them into siRNAs that turn off expression o genes with related sequences smiiarly to how miRRNAs function
Additional Evidence That DNA is the Genetic Material
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Concept 16.3 A chromosome consist of a DNA molecule packed together with proteins
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Evidence That Viral DNA Can Program Cells
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Charles Darwin and the Theory of Natural Selection:
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Concept 1.2: The Core Theme: Evolution accounts for the unity and diversity of life Grouping Species: The Basic Idea
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Forming and Testing Hypothesis
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Making Observations
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The Key Roles of Cell Division
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Cellular Orgnaization of the Genetic Material
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Deductive Reasoning
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Genomics: Large-Scale Analysis of DNA Sequences
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Theme: Life's Processes Involve the Expression and Transmission of Genetic Informaiton
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ThemeL From Ecosystem to Molecules, Ineractions Are Iportant in Biological Systems
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concept 12.2 the mitotic phase alternations with interphase in the cell cycle phases of the cell
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Chapter 12: The Cell Cycle
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Cytokinesis: a closer look
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the cell cycle control system
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Behavior of Chromosome Sets in the Human Life Cycle
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Concept 13.2 Fertilization and meiosis alternate in sexual life cycles
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Concept 13.4 Genetic variation produced in sexual life cycles contributes to evolution
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Concepts 13.3 Meiosis reduces the number of chromosome sets from diploid to haploid
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Chapter 13: Meiosis and Sexual Life Cylcle Variations on a Theme
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kinetochore
---> each of the two sister chormatids of a duplicated chormsomse has a kinetochore a structure made up of proteins that have assembled on specific section of DNA at each centromere" • the chromosomes two kinetchochores face in opp. Direction
single-strand binding proteins
--> after the parental strands separate single-strand binding proteins bind to the unpaired DNA strands, keeping the from repairing "proteins that bind to the unpaired DNA strands in order to keep them from re-pairing"
4 Steps of Huamn Development
1. a. at the end of cleave the eberyo has more than 100 cells arranged around acnetral cacity and has reached the uterus b. at this stage the emberyo is called a blastocyst (the mammal version of a blastula) c. clustered at one end of the blastocy vasity is a group called the inner cell mass which will develop into the embryo proper d. it is the cells of the very early blastocysts stage that are the soruce of embryonic stem cl lines 2. l a. embryo implantation is intiated by the trophoblasts (the outer epithelium of the blastocyst) b. enzymes secreted by the trophoblasrt during impanation break down molcules of the endometrium (the lining of the utus) allowing invasion by the blastocty c. the trophosblast also extender finger like projects that can be captured by trophoblast tissue d. around the time the mebro undergores impanantation the inner cell mase of the blastocyst forms a flat disk with an inner layer of cells-the epiblast, and an outer layer- the hypoblast e. the human embryo developsalmst entirely from epiblast cells 3. 3 a. following ompantation the trophoblast conitues to expand into the endometrium and four new mebrances appear b. although these extraembryonic membrances arise from the emebryo they enclaose specialsies structures located outside the emebryo c. as impnanation is completed gastrulation beiings d. some epbast cells remain as ectoderm on the surface while others move inward through a primtite strak and from mesoderm and endoderm 4. - a. by the end of gastrulation the embryonic germ layers have fromed b. extramebryonic mesoderm and four distinct enxtrambryonic memnraces now surround the embryo c. cells of the dinvading trophoblast. The epiblast and the adjacent endometrial tissue eas contributed to the formation of the placenta d. this vital organ mediattes the chance of nutriesnts, gases and nitgeogous wastes between the developing embryo and the mother
Chargaff Rules
1. "the base composition of DNA varies between species" 2. "for each species, the percentages of A and T bases are roughly equal and the percentage of G and C bases are roughly equal"
• the accurate translation of a genetic message requires two instancees of molecular recognition
1. a tRNa that binds to an mRNA codon specifying a particular amino acid must carry that amino acid and no other to the ribosome 2. pairing of the tRNA anticodon with the appropriate mRNA codon
tRNA that binds to mRNA must present correct aminco acid
1. a tRNa that binds to an mRNA codon specifying a particular amino acid must carry that amino acid and no other to the ribosome o the correct matching up of tRNA and amino acid is carried out by a family of related enzyme called aminoacyl-tRNA synthetases o the active site of each type of aminiacyo-tRNA synthease fits only a specific combination of amino acid and tRNA
Darwins Observations
1. indivudlas in a pop vary in their traits, many of which seem to be heirtable 2. a population can produce far ore offispring than can survive to produce offspring of their own; more individuals and less resources→competition 3. sepecifies generally suit their environemnts (adaptation)
"On the Origin of Species by Means of Natural Selection"
1. present day speciies arose from a succession of ancestors that differed from them→"descent with modification" 2. "natural selection: is an evolutionary mechanism for descent with modification
Three Events unique to meiosis occur during meiosis 1: Synapsis and crossing over
1. synapsis and crossing over: during prophase I duplicated homologs pair up and crossing over occurs a. synapsis and crossing over normally do not occurring during prophase of mitosis
Drosphila Experiment: mutations and positioanl info
1940's study of mutants to invesitage Dropshola development o established that genes contrl development and have led to an understanding of the key roles tha specific molecule splay in defining position and difrecting differentiation
homologous pairs at metephase plate
2. homologous pairs at the metaphase plate: at metaphase I of meiosis chromosomes are position at the metaphase plate as pair of homologs a. in metaphase of mitosis: individual chromosomes align on the metaphase plate
pairing of the tRNA anticodon with the appropriate mRNA codon
2. pairing of the tRNA anticodon with the appropriate mRNA codon o some tRNA mist be able to bind to more than one codon o this versatility is possible because the rules for base pairing between the third nucleotide base of a codon and the corresponding base of a tRNa anticodon are relaed compared to those at other codon position
separation of homologis
3. Separation of homologs: at anaphase I of meiosis the duplicated chromosomes of each homologous pair move toward opposite poles but the sister chromatids of each duplicated chromosome remain attacked a. In anaphase of mitosis the sister chromatids separate
key to translating a genetic message into a specific amino acid sequence
: each tRNA molecule translates a given mRNA codon into a certain amino acid • this is possible because a tRNA bears a specific amino acid at one end while at the other end is a nucleotide triplet that can base-pair with the complementary codon of mRNA
• after translation
: eukaryotic polypeptides must be processed toyield functional protein molecules o ex: cleavage of the initial insulin polypeptide forms the active hormone
• AUG has a dual function
: it codes for the amino acid methionae and functions as a start signal or initiation codon
histone
= "proteins responsible for the first level of DNA packing in chromatin" • although each histone is small containing only about 100 amino acids the total mass of histone in chromatin roughly equals the mass of DNA • more than a fifth of a histones amino acids are positively charged →bind tightly to the negatively charged DNA
Tumor
= a mass of abnormal cells within otherwise normal tissue
Proximal control elements
="located near the promoter"
• myoD (master regulatory cell)
=encodes MyoD proetien-a tranicption facot that binds to specific control element in the enhabcers of various target genes and stimulates their expression o Some target genes for MyoD encode still toher muscle-scified transtitpin factos o MyoD also stimulated pexresion of the myoD gene itself o All the genes activated by MyoD hae enchacer control elements regonzid by MyoD and are thus coordinately controlled o The secondary tranicption factors activate the genes for preotisn such as myosin and act that confer the unqieu props of skeetla muscle cells • MyoD is capable of changing some kidns of fully differntated cnonmsucle cells ; it doesn't work on all kids of cells because the activation of muscle-specific genes is not solely depdent on MyoD but requires a particular combination of regulatory proteins
organ
A body pasrt that carries out a particular function in the bod
A single gene can be transcribed simultaneously by several molecules of RNA polymerase
A growing strand of RNA trails off from each polymerase w/length of each new strand reflecting how far along template enzyme has traveled from starting place o →the congregation of many polymerase molecules simultaneously transcribing a gene genes→increases amount of mRNA transcribed→helps the cell make encoded protein in large amounts
lagging strand
to elongate the other new strand of DNA in the mandatory 5'→3' direction DNA poll II must work along the other template strand in the direction away from the replication fork " the DNA strand elongating in this direction (away from the replication fork)" o synthesized discontinuously as a series of segments
system biology
to explore emergent properties in hand with reductionism, the exploration of a biological system by analyzing the internactions among its parts
Genetically constrained cells vs totipotent stem cells
totopotent stem cells: these cells have unlimited capability to form extraembryonic membrane and tissues, the membrane itself, and all postembryonic tissues and organs ex: an embryo
Termination of Transcription bacteria
transcription proceeds through a termination sequence in the DNA o transcribed termination (an RNA sequence) functions as the termination signal→causes the polymerase to detach from the DNA and release the transcript
cell adhesion molecules
transmemrbance glycoproteins called cell adhesion molecules play a key role in cell migration by pro,oting interactions between pairs of cells • cell migration also involves the extracellular matrix
Homologous chromososes or homologs
two chromomes of a pair o Both chromsoms of each pair carry genes controlling the same inherited characteristics
Sexual Reproduction
two parents give rise to offspring that have unique combinations of genes inherited from the two parents o Offspring of sexual reproduction vary genetically from their sibilings and both parents' not exact replicas
Benign tumor
when abnormal cells remain at original sight The abnormal cells may reamin at the original sit if they have too few genrtic and cellular changes to sruve at anothersite
experiment for determining wherter the bicoid product is in fact a mrohpohen that determines the anterior end of the fly
wherter the bicoid product is in fact a mrohpohen that determines the anterior end of the fly o →found: biocid mRNA is highly concentrated at the extreme anterior end of the mature egg o after egg is fertilized the mRNA is translated into protein o the bicoid protein then diffiueses from the anterior end toward the posterior resulting in a gradient of preitnin within the early embryo, with the highest concentration at the anterior end
DNA methylation
while some enzymes methylate the tails of histone proteins a different set of enzyme can methylate certain based in the DNA itself, usually cytosine " a process in which enzymes can methylate certain based in the DNA itself"
Archibald Garrod
• 1902: Archibald Garrod was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell o the symptoms of an inherited disease reflect a persons inability to make a particular enzyme o →"inborn errors of metabolism" o ex: alkaptonuria: urine is black because it contains the chemical alkapton which darkens upon exposure to air o →most people that have enzyme that metabolized alkpaton whereas people with alkaptonuria have inherited an inability to make that metabolic enzyme
Evidence that DNA Can Transform Bacteria (Griffith)
• 1928: Federick Griffith trying to develop a vaccine against pneumonia o studying Streptoccus pneumonia( a bacterium that causes pneumonia in mammals) o Griffith had two strains of the bacterium one pathogenic (disease causing) and one nonpathogenic (harmless) o When he killed the pathogenic bacteria with heat and then mixed the cell remains with living bacteria of the nonpathogenic strain some of the living cells became pathogenic o →this newly acquired trait of pathogenicity was inherited by all the decsendents of the transformed bacteria o →transformation
Heshey and Chase -->T2 Experiment Conclusion
• 1952 Alfred Hershey and Martha Chase performed experiemnts showing that DNA is the genetic material of a phage known as T2 o T2: one of many phages that infect E. coli
Cracking the Code
• 61 of the 64 triplets code for amino acids • the three codons that do not designate amino acids are "stop" singals or termination codons making the end of translation
Development of cancer
• A single cell in a tissue undergoes the first changes of the multipstep pcess that convers a normal cell to cancer cell • Such a cell often has altered proteins on its surface and the bodys immune system normal recognizes the cell as nonself and destroys it o If the cell evades destruction it may proliferate and form a tumor
Differential Gene Expression
• A typical human cell may express about 20% of its protein-coding genes at any given time o Highly differential cells express an even smaller fraction of their genes • Almost all the cells in a multicellular organism contain an identical genome but the subset of genes expressed in the cells of each type is unique→cells to carry out their specific function • The difference between cell types therefore due to differential gene expression
spreading of cancer cells
• Abnormal changes on cell surgace cause cancer cells to lose atachments to toher cells and the extraceullular matrix; allowing them to spread into nearby tissue • A few tumor cells may spate from the original tumor, enter blood vessels and lympth vessles and spread
abnormal cell cycle control system
• Abnrality is almost always a change in one or more genes that alters the function of their protein products, result in faulty cell cycle control • If and when theys top diving cancer cells do so at random ppint in the cycle rather than at the ormal checkpints • Cancer cells can go on diing indeinfitely in culture I f they are given a continual supply of nutrients
Main Stages of Embryonic Development (Fertilization, Cleavage, gastrulation, organogenesis)
• Across a rnage of animal speciies embryonic deve;opment involves common stages that occur in a set order: o Fertilization: the fusion of sperm and egg o Cleavage state: a series of cell divisons dive, or cleave the embryo into many cells→generate a hollow ball of celled called balssturla o Gastrulation: blastula fold in on itself- rearranging into a multilayered embro, the gastrula o Organogenesis: local changes in cell shape and alrge-scale changed in cell location generate the rudiemantry organs from which adult srtucutres grow
purines
• Adenine and guanines are purines= "nitrogenous bases with two organic rings"
cytoplasmic determinants and early cell development
• After fetilication early mitttic division distributed the sygotes cytoplasm into separate cells o The nuceli of these cells may be exposed to different cytoplasmic determiannted depending on which protions of the zygotic cytoplasm a cell received o The combination of cytoplasmic determianted in a cell helps determined its develolental fate by regulating expression of the cells genes during the course of cell differentiation
Crossing Over and Synapsis During Prophase I
• After interphase the chromosomes have been duplicated and the sister chromatids are held together by proteins called cohesis • Early in prophase I: the two members of a homologs pair associate loosely along their length • Each gene on one homolog is aligned precisely with the corresponding gene on the other homolog • The DNA of two non-sister chromatids is broken by specific proteins at precisely corresponding points • The formation of a zipper- like structure called the synaptonemal complex hold one homolog tightly to the other
eukaryotes-->Eukarya (kingdom plnatae, animalia, fungi)
• All the eukarypote are now grouped in domain Eukarya o Kingdom Plantae-rpduce their own sugars and other food olecules by photosynthesis o Kingdom Animalia -obtian foods by eating and digsting other orgnaisms o Kingdom Fungi-absorb dissolved nutrients from their surrounds o Distinguished by their modes of nutrion
differential gene expression
• All three processes rooted in cellular behavior • Almost all cells in an organism have the same genomel therefore differential gene expression results from the genes being regulated differently in each cell type
DNA Structure
• Already known that DNA is a polymer of nucleotides, each consisting of three components; a nitrogenous base, a pentose sugar called deoxyribose and a phosphate group o The base can be adenine (A), thymine (T), guanine (G), or cytosine
DNA methylnation pattern disruption affects
• Alterations in normal patterns od DNA methylation are seen in some cancers
Anaphase
• Anaphase does not begin until all the chromosomes are properly attached to the spindle at the metaphase plate o As long as some kinetochores are unatcahec to spindle microtubules the sister chromatids reamin together and delay anaphase o Only when the kinetochore of all the chromosmes are properly attached to the spindle does the appropriate regulatory protein complex become activated • Once activated the compex sets off a chain of molecular events that activates the enzyme separase (cleabes the cohesis) allowing th sister chromatids to seprate o Mechanism ensures that daughter cells do not end up w/missing or extra chromosms
Stop and Go Signs: Internal and External Signals at the Checkpoints
• Animal cells genrally have built-in stop signals that halt the cell cycle at checkppints until overridden by go-ahead signlas • May signals egisted at checpoints some from cellular sureveillance mechniams inside the cell o These signlas report whether crucial cellular processes that should have occurred by that ppoint have in fact been completed correctly and thus wehter or not the cell cycle should proceed o Checkpoints also register signals from outside the cell
methylation and DNA replication
• At DNA sites where one stand is already methylated enzymes methylate the correct daughter strand after each round of DNA replication o Methylation patterns are thus passed on and cells from iing specialized tissues keep a chemical record of what occurred during embryonic development o This methylation pattern accounts for genomic imprint in anims
Bacteria: RNA polymerase
• Bacteria have a single type of RNa polymerase that synthesizes not only mRNa but also other types of RNA that function in protein synthesis such as ribosomal RNA
Chargaff
• Biochemist Chargaff analyzed the base composition of DNA from a number of different organism o The base composition of DNA varies from one species to another o →made DNA a more credible candidate for the genetic material o noticed a peculiar regularity in the rations of nucleotide bases: the number of adenines approximately equaled the number of thymine and the number of guanines approximately equaled the number of cytosines
Concept 18.2 Eukaryotic gene expression is regulated at many stages
• Both unicellular organism and the cells of multicellular organisms continually turn genes on and off in response to signals from their external and internal environments • Regulation of gene expression is also essential for cell specialization in multicellular organisms o To perform its own distinct role: each cell type must maintain a specific program of gene expression in which certain genes expressed and others not
Chapter 47: Animal Development A Body Building Plan
• By combining molecular genetics with classical embryology developmental biologists have learned a great deal about the transformation of a fertilized egg into an adault • Examining embryo from a range of species has revealed common features at early stages • Researchers have demonstrated that sepcici patterns of gene expression in a developing embryo direct cells to adopt distinct fates • Even animals that display widely differing body plans share many basic mechanisms f develooment and often use a common set of regulatory genes • Model organisms: spciecies chosen for the ease with which they can be studied in the lab
Fact block to polyspermy
• By preventing additional sperm from fusing with the eggs plasma membrance this depolarization ascts as the fast block to polyspermy ="depolarization that prevents additina sperm from fusing with the eggs plasma membrance "
Loss of cell cycle controls in cancer cells
• Cancer cells do not heed the normal sgnlas that reulat the cell cycle • In culture they do not stop divind when growth factors are depleted o Cancerr cells do not geed growth factors in their culture medium to grown and divide o They may make a rewuire dgrowth factor themselves or have an aborna,ity in the singlaing pathway that conveys thr growth facors signal to the cell cycle control system even in the ase of that factor o Another possibility: abnormal cell cycle control system
development of a cell
• Cells organized into tissues→tissues→organs→organ systems→whole organism • Any developmental program must produces cells of different types that form higher level structures arranged in a particular way in three dimensions
Regulation of Transcription Initiation
• Chromatin modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery • Once the chromatin of a gene is optimally modified for expression the initiation of transcription is the next major step at which gene expression is regulated • Bacteria: the regulation of transcription initiation in eukaryotes involving proteins that bind to DNA and either facilitate or inhibit biding of RNA polymerase • Process is more complicated in eukaryotes
Crick and DNA X-Rays
• Crick was studying protein structure with a technique called C-ray crystallography o While visiting the laboratory of Maurice Wilkins, Watson saw an X-ray diffraction image of DNA produced by Wilkin's accomplished colleague Rosalind Franklin o →the spots and smudges in the C-ray were produced by X-rays that were diffracted as they passed through aligned fivers if purified DNA
pyrimidines
• Cytosine and thymine are pyrimidines= "nitrogenous bases with one single ring"
Characterisitics of DNA methylation
• DNA methylation occurs in most plants, animals and fungi • Long stretches of inactive DNA are generally more methylenated than regions of actively transcribed DNA • On a smaller scale individual genes are usually more heavily methylated in cells in which they are not expressed • Removal of the extra methyl groups can turn on some of these genes • One methylated genes usually stay that way through successive cell divisions in a given individual
Chromatin and gene expression
• DNA of eukaryotic cells ic packaged with proteins in an elaborate complex known as chromatin • The structural organization of chromatin not only packs a cells DNA into a compact for that fits inside the nucleus it also helps regulate gene expression in several ways
DNA polymerase: directionality of additional nucleotides (Leading strand)
• DNA polymerase can add nucleotides only to the free 3' end of a primer or growing DNA strand, never to the 5' end o A new DNA strand can elongate only in the 5'→3' direction o Along one template strand DNA polymerase II can synthesize a complimentary strand complimentary strand continuously be elongated the new DNA in the mandatory 5'→3' direction o DNA polymerase III continuously adds nucleotides to the new complementary strand as the fork progresses o →the DNA strand made by this mechanism is called the leading strand
The Evolutionary Significance of Genetic Variation Within Populations (DARWIN)
• Darwin: a population evolves through the differential reproductive success of its variant members o On average those individuals best suited to the local environment leave the most offspring thereby transmitting their genes o Natural selection results in the accumulation of genetic variations favored by the environment o As the environment changes the population may survive- at least some of its members can cope effectively with the new conditions
density-dependent inhibition and anchorage
• Density-dependent inhubution and anchorage dependes appear to function ot only in cell cutlrue but also in the bodys tissues o Checking the growth of cells at some optimal density and location during embryonic development and throughout an organisms life
Morphogenesis:
• Different kinds of cells not randomly stsiftubuted but are organized into tissues and organs in a particular 3-D arrangement • The phusucical processes that give a orgnaizsm its shape consiute morphogenesis ="the development of the form of an organism and its structures"
diversity
• Diversity can occur because each cell type contains a different group of activator proteins • Athough the cells of an embryo all arise from one cell diverse paths during embryonic development lead to different sizes of activator proteins in each type of cell→184. Depicts how these cells come to differ
ex interactions with organisms-->glucose and blood sugar
• EX: AFTER MEAL LEVEL OF SUGAR CGLUCOSE RISES→INCREASE IN BLOOD GLUCOSE STIMULATED PANCREALSE TO RELASE INSULIN TO BLOOD→INCE T REACH LIVER OR MUSCLE CELLS INSCULIN CAUSES EXCESS GLUS STORED IN FROM OF GLYCOGEN--?reducing blood clguglae leel to range that is compotmal for bodily function→lower blood glulcose result sno ligner stimulated isnlguin secretion by pancreac cells
Human DNA Replication
• Each of human cells has 46 DNA molecules in its nucleus o One long double-helical molecule per chromosome o Represents about six billion nucleotide pairs • It takes one of human cells just a few hours to copy all of this DNA o This replication of genetic information is achieved with very few errors- only about one per ten billion nucleotides • More than a dozen enzymes and other proteins participate in DNA replication o →most of the process in fundamentally similar for prokaryotes ad eukaryote
epigenetic variations insight into genetic illnesses
• Epigenetic variations might help explain why one identical twin acquires a genetically based disease but the other does not despite their identical genome
Proofreading and Repairing DNA
• Errors in the complete DNA molecule amount to only one in tten billion nucleotides→100,000 times lower o Why? b/c during DNA replication DNA polymerases proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand o →upon finding an incorrectly paired nucleotide the polymerase removes the nucleotide and then resumes synthesis • mismatched nucleotides sometimes evade proofreading by a DNA polymerase
eukaryotes three types of RNA polymerase
• Eukaryotes have at least three types of RNA polymerase in their nuclei o The one used for pre-mRNA synthesis is called RNA polymerase II o The other RNA polymerases transcribe RNA molecules that are not translated into protein
Combinatorial Control of Gene Activation
• Eukaryotes: the precise control of transcription depends largely on the biding of activators to DNA control elements • A dozen or so short nucleotide sequences appear again and again in the control elements for different genes • On average: each enhancer is composed of about ten control elements, each of which can bind only one or two specific transcription factors o It is the particular combination of control elements in an enhancer associated with a gene that is important in regulating transcription of the gene • Even with only a dozen control element sequence available a very large number of combinations are possible o Each combination of control elements will be able to activate transcription only when the appropriate activator proteins are present
Experimental Vairables and Controls
• Experiment involes a manipilaion of one factor in a system in order to see the effects of changing it; both the favtor manipulated and the effects measured are types of experimental vairbales
fertilization-->initates and speeds up metabolic ractions
• Fertilization intiates and speeds up metabolic rections that trigger the onset of embryonic development
Fertilization (Steps of fertilization)
• First: sperm dissolve or prentrate any protective layer surrounding the effd to reach the plasma mebrance • Next: molecules on the sperm suface bind to receports on the egg surface • Finally: changes at the surface f the egg prevent polyspermy- a codnition in which multiple sperm nueli enter the egg, fatally disrupting development • The cell surface events that take place during fertilization has been studied most extensively in search urchins
tissue to work effectively
• For the issues to function effectlyilv in the organism as a whole the orgnaismis body plan—its overall three dimesneion arrangement—must be established and superimposed on the differentiation process
The Flexibility of the Scientific Process:
• Forming and Testing Hyptheses, Exploration and Discovery, Community Analysis and Feedback and Scoeital Benefits and Outcomes all interplay
Rotations of DNA and nitrogenous bases of double helix orientation
• Franklins X-ray data indicated that the helix makes one full turn every 3.4 nm along its length o There are ten layers of base pairs in each full turn of the helix • The nitrogenous bases of he double helix are paired in specific combinations: adenine with thymine and guanine with cytosine
Theme: Life Rqures the Transfer and Tranformation of Energy and Matter
• Fundemntal charatceits of loving organisms is their use of energy to carry out lifes acitivies • The chemical energy in the food molcules then passed along by plants and other photosynsthen organisms (producers) to consumers • consumerS: orgnisms, such as animals, that feeed of porducers and other consumers • when an organisms uses chemical enegy ot perform work some of that energy is lost to the surrounds as heat • energy flows one way through an ecosystem • chemicals are recycled within an ecosystem
genetic messages beginning
• Genetic messages usually begin with AUG mRNA codon →signals the protein synthesizing machinery to begin translating the mRNA at that location o →an enzyme can remove the starter amino acid from the chain
Science, Technology and Society
• Goal of science to understand antural henomena, while techinlogy is to apply scientific knowledge for some specific purpose • Direction technology takes deende less on the curisolity that deives basic sicnece than on the cuent needs and wats of people • Ethical issues of science based on cultural values
liver cell and lens cell gene expression
• How differential gene expression occurs in two cells types, a liver cell and na lens cell o Each of these fully differentiated cells have a particular mix of specific activators that utnr on the collection of genes whose proeductis are requrid in the cells
Chapter 16: The Molecular Basis of Inheritance
• In April 1953: James Watson and Francis Crick chook the scientific world: proposing an elegant double-helical model for the structure of DNA o Gregor Mendel's heritable factors and Thomas hunt Morgans genes on chromosomes are composed of DNA • Of all natures molecules nucleic acids are unique in their ability to direct their own replication from monomers • The resemblance of offspring to their parents has its basis in the accurate replication of DNA and its transmission from one generation to the next o Hereditary information in DNA directs the development of your biochemical, anatomic, physiological and (to some extent) behavioral traits
Cell in which DNA synthesis has occurred
• In a cell which DNA synthesis has occurred all the chromosomes are duplicated and therefore each consist of two identical sister chromatids o Sister chromatids are associated closest at the centromere and along the arms
sexual vs. asexual reproduction in stable environment
• In a stable environment sexual reproduction seems as if it would be less advantageous than asexual reproduction o Sexual reproduction is more expensive energetically than asexual reproduction
gene expression controlled at transcription
• In all organisms gene expression is commonly controlled at transcription ;regulation at this stage often occurs in response to signals coming from outside the cells such as hormones or other signaling molecules o →for this reason the term gene expression is often eauted with transcription for both bacteria and eukaryotes o while may often be the case for bacteria the greater complexity of eukaryotic cell structure and function provides opportunities for regulating gene expression of many additional stages
bacteria vs. eukaryotes
• In bacteria: part of the RNA itself specifically recognizes and binds to the promoter • In eukaryotes: a collection of proteins called transcriptor factors mediate the binding of RNA polymerase and the initiation of transcription o Only after transcription factors are attached to the promoter does RNA polymerase II bind to it
12.1 Most cell division results in genetically dentical daughter cells
• In eukaryotes and porkaryotes most cell divison involbes the distruvtion of identical DNA to two daughter cells (exception is meiosis that produces sperm and eggs) o A dividing cell replicates its DNA, allocates the two copies to opposite ends of the cell, and only then splits into daughter cells
# chromosomes -->haploid
• In humans the haploid number is 23 o The set of 23 consists f the 22 autosomes plus a single sex chromosome • An unfertilized egg contains an X chromosome but a sperm may contain an X or Y chromosome
pre-mRNA splicing
• In making a primary transcript from a gene RNA polymerase II transcribes both intros and exons from the DNA BUT the mRNA that enters the cytoplasm is an abridged version o The introns are cut out from the moles and the exons bound together forming an mRNA molecules with a continuous coding sequence • Pre-mRNA splicing o The removal of introns is accomplished by splicesome
regulation
• Interactions among bodys molecules are repsnsible for ost of the steps in this procecc • The key: ability of amny viological processes to self regulate by a mechanism called feedback
genes and proteins
• Many genes provide the blupeirnts for making protections which are major in vuilding and maintain the cell and carrying out its activities o Ex: a given bacterial gene may specific a particular protein (enzyme) while guman gene may denote a different protein (antibody) • Genes control protection production indirectuly using RNA as an intermediary→the sequences of nucleotides along a gene trabsirbed into RNA--?tras;aed int a linked series of amino acids →result in a specific protein
egg materials coordination of cell development
• Materials palced into the egg by the mother set up a sequential rpgoream of gene regulation that is carried out as cells divide, and this program coordinaties cell diffetnaition during embryonic development
Matthew Meselson and Franklin Stahl
• Matthew Meselson and Franklin Stahl devised a clever experiment that distinguished between the three models devised a clever experiment that distinguished between the three models
A Comparison of Mitosis and Meiosis (Meiosis vs. Mitosis General)
• Meiosis reduces the number of chromosome sets from two (diploid) to one (haploid) whereas mitosis conserves the number of chromosome sets • Meiosis produces cells that differ genetically from their parent cell and each other whereas mitosis produces daughter cells that are genetically identical
"upstream" vs "downstream"
• Molecular biologists refer to the direction of transcription as "down stream" and the other direction as "upstream" • The promoter sequence in DNA is said to be upstream from the termination
anchorage in animal cells
• Most animals also exhibit anchorage dependence o To divde they must be attached to a substratus (such as the inside of a culture flash or the extraculluar matrix of a tussue) o Ancrhoage is signaled to the cell cycle control system via pathways involving plasma membrane proteins and elements of the cytoskeleton lnked o them
eukaryotes and splicing
• Most eukaryotes genes and their RNA transcriptions have long noncoding stretches of nucleotides-regions that are not translated o Most of these noncoding sequences are interspread between doing segments of the gene and thus between coding segments of the pre-mRNA o The sequence of DNA nucleotides that codes for a eukaryotic polypeptide is usually not continuous ;it is split into segments
cell division in multicellular eukaryotes
• Multicellular eukaryotes: cell divion enables each of these organisms to develop from a single cell the fertilized egg o Two celled- embryo is the first step in this process o Cell division continue to function in renewal and repair in fully grown multicellular eukaryotes; replacing cells that die from normal wear and tear or accidens
mutations-->the original source of variation?
• Mutations are the original source of different alleles which are then mixed and matched during meiosis
Concept 16.1 DNA is the genetic material The Search for the genetic Material: Scientific Inquiry
• Once TH Morgans group showed that genes exist as parts of chromosomes the two chemical components of chromosomes-DNA and protein- emerged as the leading canidates for the genetic material o Until the 1940's: the case for proteins seemed stronger b/c biochemists identified proteins as a class of macromolecules with great heterogeneity and specificity of function o Little was known about nucleic acid whose chem/phys properties seemed too uniform to account for the multitude of specific inherited traits • The role of DNA in heridtary was worked out in studies of bacteria and the viruses that infect them
egg cytoplasm and development
• One important source of information in early development is the eggs cytoplasm: contains both RNA and proteins encoded by the mothers DNA o The cytoplasm of an unfertilized egg is not homogenous o Messenger RNa, porteins, other susbtancs, and organelles are distbuted evely in the unfertilized egg and this unevenness has a profound impact on the development of the future embro in many species
gamete cells characteristics
• Only cells of human body not produced by mitosis are the gametes; develop from specialized cells called germ cells in the gonads- ovaries in females and testes in males • In sexually reproducing organisms gamete formation involves a type of cell division called meiosis
prokaryotes
• Organisms making up Bacteria and Archea are prokayrtoica
pattern formaiton in animals
• Pattern romation in animals begins in the early embryo when the major axes of an anmal are established o In a bilaterally sysymmetrical animal the relative postions of head and tia, right and left sides, and back and front are set up before the rogan appears
protein-mediated binding of DNA
• Protein-mediated binding of the DNA is though to bring the bound activator into contact with a group of mediator proteins which in turn interact with proteins at the promoter o These protein-protein interactions help assemble and position the initiation complex on the promoter o Protein interactions allow these two region in the DNA to come together in a very specific fashion
Nitrogenous Base-Pairing Rules
• Pruine (A and G) are about twice as wide as pyrimidnes (C and T) • A purine-purine pair is too wide and a pyrimidine-pyrimidine pair is too narrow to account for the 2 nm diameters of the double helix • A pairing of a purine-pyrimidne always works • Each base has chemical side groups that can form hydrogen bonds with its appropriate partners: adenine can form two hydrogen bonds with thymine and only thymine; guanines form three hydrogen bonds wth cytosine and only cytosine • Wherever one strand of a DNA molecules has an A, the partner strand had a T; wherever a G in one strand is always paired with a C in the complementary strand
RNA Processing
• RNA processing in the nucleus and the export of mature RNA to the cytoplasm provide several opportunities for regulating gene expression are not available in prokaryotes
The Three Domains of Life
• Scientisits classify the diversity of life forms into specieis and broader groupings by careful comparisons of structure, function and other obvius features • the six to twelve kinggdoms are put into broaders classifications called odmians o Bacteria o Archaea o Eukarya
repressors different ways of inhibit gene expression
• Some activators and repressors act indirectly by affecting chromatin structure • Studies using yeast and mammalian cells show that some activators recruit proteins that acetylate histones near the promoters of specific genes→promoting transcription • Some repressors recruit proteins that remove acetyl groups from histones →reduced transcription
specific transcription factors that function as repressors: ways to inhibit gene expression
• Specific transcription factors that function as repressors can inhibit gene expression in several different ways • Some repressors bind directly to control element DNA blocking activator binding • Other repressors interfere with the activator itself so it cant bind the DNA
The recongtion event etween the sperm and egg triggers fusion of their plasma mebrace
• Sperm nucleus enters the egg cypolasm as ion channels open in the eggs plasa memrbance • Sodium ions diffuse into the egg and cause depolication
DNA-->chromosomes
• The DNA of a eukaryotic cell is packaged into chromosomes within the nucleus o Every species has a characteristic number of chromosomes • One chromosome includes several hundred to a few thousand genes- each of which is a specific sequence of nucleotides within the DNA molecule
Epigenetic Inheritance
• The chromatin modification do not entail a change in the DNA sequence yet they still may be passed along future generation of cells
Gene Expression and functionality of cell
• The function of any cell depends on the appropriate set of genes being expressed • The transcription factors of a cell must locate the right genes at the right time o When gene expression proceeds abnormally serious inbalance and disease can arise
pattern formation signals
• The molecular cues that control pattern formation are roovuded by cytoplasmic determinant and inductive signals o These cues tell a cell its location relativr o the body axes and to neighboring cells and determine how the cell and tis progeny will respond to future molecular signals
environment around the cell and development
• The other important source of development information is the environment around a particular cell o Most influence: th signlas impinging on an embryonic cell from other embryonic cells in the vicinity, including contact with cell-sufrace moleucles on neighboring cells and the binding of growth factors secrete by the neighboring cells o →such singals caused changes in the target cells
fertilization and meiosis characteristics (importance)
• The process of fertilization and meiosis are the hallmarks of sexual reproduction in plants, fungi and protists as well as in animals • Fertilization and meiosis alternate in sexual life cycles→maintaining a constant number of chromosomes from one generation to the text
RNA Polymerase Binding and Initiation of Transcription
• The promoter of a gene includes within it the transcription start point + typically extends several dozen or more nucleotide pairs upstream from the start point
A Genetic Program for Embryoinic Development (3 Main Processes for Development)
• The remebakralble transmfraiton results from three interrelated processes: o Cell division o Cell differentiation o Morphogeneisis
Evolution, the Cire Theme of Biology:
• The scientific explanation for this unity and viersity is evolution: the concept that the orgnaisms living on Earth today are the modified descendents of common ancestors • The sharing of traits by two orgaisms with thepremise that the oanisms have dwcended from a common ancestor + account for difernce with the idea that heirtable changes hae occurred along the way.
X,Y Chromosomes
• The two distinct chromosomes referred to as X and Y are an important exception to the general pattern of homolgous chromosomes in human socmatic cells • Human females have a homolgous air of X chromomes (XX) • Human males have one X and one Y chromosomes (XY) • Only small parts of the X and Y are homologous • Most of the gener carried on the X chromosome do not have countwrparts on the tiny Y • The Y chromosome has genes lacking on the X
The DNA Replication Complex
• The various proteins that participate in DNA replication actually form a signle large complex, a " DNA Replication Machine" • Many protein-protein interactions facilitate the efficient of this complex o Ex: by interacting with other proteins at the fork, primase apparently acts as a molecular brake, slowing progress of the replication fork and coordinating the placements of primers and the rates of replication on the leading and laggings strands • The DNA replication complex may not move along the DNA: the DNA may move through the complex during the replication process o In eukaryotic cells multiple copies of the complex may be anchored to the nuclear matrix
RNA responsible for structure and function of ribosome
• There is strong evidence supporting the hypothesis that RNA and not protein primarily responsible for both the structure and the function of the ribosome o The proteins support the changes of the rRNA molecules as they carry out catalysis during translation o rRNA is the main constituent of the A and P sites and of the interface between the two subunits and also acts as the catalyzes of the peptide bond formation
cell division and differentiation
• Through a succession of mitotic cell dviions the zygtone gives rise to a large number of cells • Cell division alone however would merely produce a great ball of idneitical cells;nothing like a tad pole • During embryonic development cells not only increases in number but also undergo cell differentiation
The Roles of Transcription Factors (Overall)
• To initiate transcription eukaryotic RNA polymerase requires the assistance of transcription factors o Some transcription factors are essential for the transcription of all protein coding genes
Transmission of hereditary traits + DNA
• Transmission of hereditary traits has its molecular basis in the replication of DNA→produces copies of genes that can be passed from parents to offspring
A Case Study in Scientific Inquiry: Investigating Coat Coloration in Mouse Populations
• Two populaitons of mice that belong to the same spcies but have different color patterns that reside to different environment o Beach mouses lives along flordia seashore (white sand→adapted white color) o The inland mouse lives on darker, more fertile soil(dark land→adapted darker color) o Natural predators are the same o Tested (Hopi Hoeskra) whether or not mice with coloration that did not match their habitat would be preyed on more heavily than the native, well-matched mice o Control group: mouse models resembling native mice in habitat o Experimental group: models with the non-native coloration o Camoflouged models experienced less predatorial nature
haploid cell
• Unlike somatic cells gametes contain a single set of chromosomes o Such cells are called haploid cells "cells that contain a single set of chromosomes; gametes, each has a haploid number of chromosomes n"
Watson and Crick Model
• Watson and Crick began building models of a double helix that would conform to the X-ray measurements and what was then known a the chemistry of DNA (including Chargas rule of base equivalence) • Watson and Crick Model: the two sugar-phosphate backbones are antiparallel (their subunits run in opposite directions)
chromosomes and inheritance
• We inherit one chromosomes of a pair from each parent o Two sets of 23 chromosomes, one a maternal set and the other a patenrla set
cell division in prokaryotic cells and unicellular eukaryotes
• When a prokaryotic cell divides is reproducing since process gives rise to a new organism • Same is true of any unicellular eukaryote (i.e. amoeba)
MPF and Cyclins
• When cyclins that accumulate during G2 associate with Cdk molecule the resulting MPF complex ohosphorylates a varity of proetins initating mutoss • MPF acts boher directly as a kinase and idirectly by activating other kinases • MPF contributes to molecular vents required for chromose condensation and spindle formation during prophase • During anaphase MPF helps swtich itself off by intiating a process that leads to the destruction of it own cyclin • The non cyclin part of MPF , the Cdk, persists in the cell inactive until it becomes part of MPF again by associating w/ nee cyclin molivles syntehsied during S and G2 ohases of the next round of the cycle
Nutritional Mutants in Neurospora: Scientific Inquiry
• a breakthrough in demonstrating the relationship between genes and enzymes came at Stanford University-Beadle and Tatim began working with a bread mold, Neurospora o bombarded the bread with x-rays shown in the 1920s to cause genetic changes and then looked among the survivors for mutants that differed in their nutritional needs from the wild-type bread mold o wild type neurospora has modest food requirements: can grow in a lab on a simple solution of inorganic salts, glucose and the vitamin biotin, incorporated into agar (a support medium) • →the mold cells use their metabolic pathways to produce all the other molecules they need o identified mutants that could not survive on minimal medium b/c they were unable to synthesize certain essential molecules from the minimal ingredients o took samples from the mutant growing on complete medium and distributed them to a number of different vials • each vial contained minimal medium plus a single additional nutrient o the particular supplements that allowed growth indicted the metabolic defect • ex: if the only supplemented vial that supported growth of the mutant was the one fortified with the amino acid arginine they would conclude that the mutant was defective in the biochemical pathways that wild type cells use to synthesize arginine o →determined different classes of mutants • mutants in each class required different set of compounds along the arginine-synthesize pathways • →each class was blocked at a different step in this pathways because mutants in that class lacked the enzyme that catalyzed the blocked step o b/c each mutant was defective in a single gene-taken together the collected results provided strong support for a working hypothesis of one gene one enzyme
Gastrulation
• a dramatic reognriation of the hollow blastula into a two layered or three layered embryo called a gastrula • in the late gastrula the ectoderm forms the outer adyer and the endeomer lines the embryonic disestive compartment of tract • in cindirians: only these two germ layer from during gastrulation • verterbates and other animals with bilateral suyetry: require a third germ laer→triplonaladts
mirNA
• a longer RNA precursor is processed by cellular enzymes into an miRNA ="a single stranded RNA of about 22 nucleotides that form a complex with one or more proteins" o allows the complex to bind to any mRNA molecule with at least seven or eight nucleotides of complementary sequence o the miRNA protein comples then either derades the target mRNA or blocks its translation o expression of at least half of all human genomes may be regulated by miRNAs
mRNA and tRNA (codons-->amino acids-->proteins)
• a mRNA molecule is moved through a ribosome an amino acid will be added to the polypeptide chain whenever the codon for that specific amino acid translated is presented for translation • codon by codon the genetic message is translated as tRNAs deposit amino acids in the order presibreibed and the ribosome joins the amino acids into a chain • the tRNA molecule is a translator in the sense that it can read a nucleic acid word (the mRNA codon) and interpret it as a protein word (the amino acid)
pRNA's
• a newly discoerec lass of small ncRNAs is called piwi-interacting RNA's or piRNA's o these RNAs also undicue formation of heterochromatin-blocking expression of some parasticn DNA elements in the genome known and transposons =usually 27-31 nucleotides in length they are processed from a longer, single-stranded RNA precursor" o play an indispensible role in the germs cells of many animal species where they appear to help resatablish methylation patterns in the genome during gamete formation
second set of bands of cells that migrate (somites)
• a second set of migratory cells is formed when groups of cells located in strips of mesoderm lateral to the notchord separate into blocks called somites o the somites are arranged serially on both sides alojg the length of the notchord o sometimes paly a significant role in organizing the segement structure of the verteberte body o parts of the somites disocate into mesenchume cells which mgrate idnvidually to new locations o some of these cells from the vertebtrate o somite cells that become mesenchunal also form the muscles associated with the veterbral colum and the ribs
tRNA
• a tRNa molecules consist of a single RNA strand that is only about 80 nucleotides long o b/c of the presence of complementary stretch of nucleotide base that can hydrogen-bond to each other this single strand can fold back on itself and from a molecule with a three-dimensional structure o the loop of the L structure of the single strand that extends from one end of the : includes the anti codon o from the other end of the L shaped tRNA molecule protrudes its 3' end -attachment site for an amino acid
costs of behavior
• adjustments to physiology • allocation of energy for swimming • increased probability of mortality during migration
DNA polymerase I and DNA ligase on the okazaki fragments
• after DNA pol III forms an Okazaki fragment another DNA polymerase (DNA polymerase I) replaced the RNA nucleotides of the adjacent primer with DNA nucleotides • DNA polymerase I cannot join the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the adjacent Okazaki fragment o Another enzyme, DNA ligase, accomplishes the task of joining the sugar phosphate backbones of all the Okazaki fragments into a continuous DNA strand
post-cleave
• after celeave the rate of cell division slows considerably as the normal cell cyle is restored • the last two stages of embryonic deveopmnet are responsible for morphogenesis
the characteristics all cells share
• all cells share certain characetieriscs o ex: every cell is enclosed by a membrane that regulate the passage of meatierlas between the cell and its surroundigns
results of insetions, deletions and freamshift mutaitons
• all nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive messense usually ending sooner or later in nonsense and premature termination • unless frameshift very near the end of the gene the protein is almost certain to be nonf-unction
free and bound ribosomes
• all ribosomes themselves are identical and can alternate between being free one time they are used and bound the next
Cell Migration in Organogeneisus (2 sets)
• although organogeneisus requires local cellular itneractiond ansd acitivites some cells undergo long-range mrigration o ex: two sets of cells that develop near the neural tube of bertbate embryos migreate in the bbody before assuming their evelopmental fate
Elongation of the Polypeptide Chain
• amino acids are added one by one to the previous amino acid at the C terminus of the growing chain • each addition involves the participation of several proteins called elongation factors and occurs in three step cycle
bicoid and development
• an embryo or larva whose mother has two mutant iocid alleles lacks the front hald of its bodyand has [osterior strucutrss and both ends • the product of the mother biocid genes Is essential for setting up the anterior end of the fly ad might be concentrated at the future anterior end of the embryo
X-Ray Photo's: DNA Structure
• an examination of the photo that Wilkin showed him confirmed that DNA was helical in shape • an examination of the photo also suggested the width of the helix and the spacing of the nitrogenous bases along it • an examination of the photo also implied that the helix was made up of two strands
mRNA and DNA template
• an mRNa molecule is complementary rather than identical to its DNA template b/c RNA nucleotides are assembled on the template according to base-pairing rules o these pairs are similar to those that form during DNA replication expect that U pairs with A and the mrNA nucleotides contain ribose instead of deoxyribose the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA
Crossing Over
• as a consequence of the independent assortment of chromosomes during meiosis: each of us produces a collection of gametes differing greatly in their combinations of the chromosomes we inherited from our two parents • each chromosome in a gamete is exclusively maternal or paternal in origin o this is NOT the case because crossing over produces recobinatnt chromosomes
signs of differentiation (observable cell differentiation)
• as the tissues and organs of an embryo develop and their cells differneitaiton the cells become more noticieably different in structyre and function • the outcome of determination—observake cell differentiation—is marked by the expression of genes for tissue-specific protein
structure and function
• at ach level of biologicl hierarchy you find a correlation of structure and function • analyzing a biological struction gives us clues about what it does and how it works, knowing the function provides insight into structure
EconsysemsL An Orgnisms Interactions with Other Organisms and the Physical Environment
• at the ecosystem level, each orgnisms interacts with other organisms o sometimes interactons between organism mutuerally beenefical (think cleaner fish and turtle) o sometimes interactons between organism allows one harmed and one benefited (thnk lion and era)
maternal affect gene (egg-polarity genes)
• because they control the rogientaiton (polarity) of the egg and of the fly thse maternal effect genes are also called egg-polarity genes o one group fo these sgenes set up the anterior-posterior axis of the embryo wihile a seconf group establsied the dorsal-vetnral axid o mutatiosn in these genes are generally embryonic lethals
replication and distibution of DNA
• before the cell can divdde to form genetically identical daughter cells all o f DNA must be copied and then two copies sep. so each daughter cell ends up w/ complete genome • replication/distrubtion of DNA possible b/c DNA molecules packaged into chromosomes • eack eukaryotic chromosome consists of one very long linear DNA molecules associated w/ many proteins • the DNA molecules carries several hundred to a few thounsa genes which specify an organism inherited traits • the associated protein main trhs tructure of the chormosom and help control activit y of the genes
Neurulation (notochord, neural plate, induction)
• begins as cells from the dorsal mesoderm form the notochord • notchord: a rod that extends along the dorsal side of the chordate embryo • signaling molecules secreted by these medoserm cells and other tssues cause the ectoderm abve the notchord to become the nural plate • formation of the nueral plate is an example of induction • induction: a process in which a group of cells or tissues influence the development of another group through close-range interactions • after the ntuerla plate is formed its cells change shapre curving the structure inward
histone modification and gene expression
• chemical modifications to histones play a direct role in the regulation of gene transcription o the N-terminus of each histone molecule in a nucleosome protrude outward from the nucleosome o the histone tails are accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups o histone acetylation appears to promote transcription by opening up the chromosome structure while addition of methyl groups can lead to the condensation of chromatin and reduced transcription
chromatin changes during cell cycle: interphase chromatin vs. mitotic chromatin
• chromatin undergoes striking changes in its degree of packing during the course of the cell cycle o interphase: the chromatin usually appears within the cells as a tissue mass within the nucleus →chromatin is highly extended o as a cell prepares for mitosis its chromatin coils and fold up →a characteristic number of short, thick metaphase chromosomes • though interphase chromatin is less condensed than mitotic chromatin it shows several of the same levels of high-order packing • interphase chromosome does not have scaffold but looped domains appear to be attached to the nuclear lamina on the inside of the nucleus envelop and to fibbers of the nuclear matric o these attachments may help organize regions of chromatin where genes are active • the centromeres and telomeres of chromosomes exist in a highly condenses state similar t that seen in a metaphase chromosome
Cleavage Patterns in Amphibians
• cleavage in ampiabial development is therefore said to be hobolastic • hobolastic cleave is also seen in many other groups of animals including echniderms, mammalains, an anneids o in those animals whose eggs contain a relatively little amount of yolk, the blastocoel forms centrally and the blastomeres are often of similar size
co-expressed eukaryotic genes
• co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathways, are typically scattered over different chromosomes • here: coordinate gene expression depends on the association of a specific combination of control elements with eeru gene of sa sipered group • activator proteins in the nucleus that recognize the control elements bind to them→promoting simultaneous transcription of the genes no mater where thy are in the genome • coordinate control od dispered genes in a eukaryotic cell often occurs in response to chemical signals from outside the cell o ex: a steroid hormone enters a cell and binds to a specific intercellular report protein , forming a hormone-receptor complex that serves as a transcription activator o every gene whose transcription is stimulated by a particular steroid hormone regardless of its chromosomal location, has a control element recognized by that hormone receptor complex o this is how estrogen activates a group of genes that stimulate cell division in uterine cells
cytoplasmic determinants and axon establishment
• cytoplasmic determinants in the egg are ths usbtances that initially established the axes of the Dropshila body o these susbtances are encoded by genes of the mother, fittingly called maternal effect genees
favorable factors
• decreased predation • decreased disease • decreased physiological stress • Increased food availability
differentiated cells: specialists at making tissue-specific proteins
• differentiated cells are speacilaists at making tissue-specific proteins o ex: as a result of trandciptioanlr egulation lver cells specialized in making albumin and lens cells epcailzed in making crystalline o ex: sketleta muscle cells in vertebrates: each of these cells ia s long fiver containing many nueli within a single plasma membrane; have high concentrations of muscle-speicfic bversions of the contractile proteins myosin and actin as well as membrace reception protins that detect signals from nerve cells
general overview
• during interphase in animal cells the single centrosome durplications→two centrsoms→remain in nucleus→move apart during prophase and prometraphse→spinlde microtubules grow out from them→end up at opp.end of cells • an aster extends from each centrosome • the spindle indlcudes the centrosoms, the spindle microtubules and the asters
Protein Folding and Post-Translational Modification
• during its synthesis a polypeptide chain begins to coil and fold spontaneously as consequence of its amino acid sequence o →forming a protein with a specific shape: a three dimensional molecule with secondary and tertiary structure o a gene determine primary structure and primary structure in turn determines shape
Organogenesis
• during organogenesis regions of the three embryonic germ layers develop into the rudeiments of rogans • often cells from two or tree germ layers pariculation in formation of a single organ with internactions between cells od ifferenct germ layers hekping to specify cell fates • adoption of partuclar developmental fatres may in turn cause cells to change shapre or in certain cirumstances mrigrate to another location in the body
translation
• during translation the sequence of codons along an mRNA molecule is decoded or translated into a sequence of amino acids making up a polypeptide chain o the codons are read by the translation machinery in the 5'→3' direction along the mRNA o each codon species which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide o the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product
Nuclear Architecture and Gene Expression
• each chromosome in the interphase nucleus occupies a distinct territory but the chromosomes are not completely isolated however • crosslink and identity regions of chromosomes that associated with each other during interphase: these studies reveal that loops of chromatin extend from individual chromosomal teritoeis into specific sites in the nucleus o different loops from the same chromosome and loops from the other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription-associated proteins o these so called transcription factories are thought to be areas specialized for a common function
Alteration of mRNA ends
• each end of a pre-mRNA molecule is modified in a particular end o the 5' end receives a 5'cap o the 3' end also modified before the mRNA exists the nucleus; at this end an enzyme then adds 50-250 mores adenine nucleotides forming a poly A-Tail
DNA biochemical sugar phosphate structure
• each nucleotide to be added to a growing DNA strand consist of a sugar attached to base and to three phosphate groups o the only difference between the ATP of energy metabolism and dATP, the adenine nucleotide used to make DNA, is the sugar componment, which is deoxyribose in the building block of DNA but ribose in ATP o the nucleotides used for DNA synthesis are chemically reactive partly b/c of their triphosphate tails having an unstable cluster of negative charge o as each monomer joins thee growing end of a DNA strand, two phosphate groups are lost as a molecule of pyrophosphate o subsequent hydrolysis of the pyrophosphate to two molecules of irnogance photospate is a couple exergonic reaction that helps drive the polymerization reaction
DNA, the double helix
• each ribbon representing one of the sugar-phosphate backbones • phosphate groups along the backbone contribute a negative charge along the outside of each strand • the TEM shows a molecule of naked (protein-free)DNA;the double helix alone is 2nm across
Termination of Translation
• elongation continues until a stop codon in the mRNA reaches the A site of the ribosome • the nucleotide base triplets UAG UAA UGA do not code for amino acids but instead act as signal to stop translation • a release factor binds directly to the stop codon in the A site
Synthesizing a New DNA Strand (DNA polymerase)
• enzymes called DNA polymerase catalyze the synthesis of new DNA by adding nucleotide to a preexisting chain
results of errors made during DNA replication or recombination
• errors during DNA replication or recombination can lead to nucleotide pair substitutions, insertions, or deletions as well as to mutations affecting longer stretches of DNA • if an incorrect nucleotide is added to a growing chain during replication the base n that nucleotide will then be mismatched with the nucleotide base on the other strand • in man cases the error ill be corrected by DNA proofreading and repair systems o if not: the incorrect base will be used as a template in the end round of replication, resulting mutation
eukaryotes and RNA polymerase II transcribe process
• eukaryotes RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence→species (AAUAAA) in the pre-mRNA o at a point further down these proteins cut it free from the polymerase releasing the pre-mRNA o pre-MRNA then undergoes processing o the RNA polymerase II continues to transcribe o since new end isn't protected by a cap enzymes degrade the RNA from 5'end o polymerase continues transcribing pursued by the enzymes
eukaryotic ribosome
• eukaryotic ribosomes are slightly larger as well as different somewhat from a bacterial ribosome in the molecular composition o ex: certain antibiotic drugs can inactivate a bacterial ribosomes without affecting eukaryotic ribosomes
eukaryotic cell
• eukaryptic cell: contains membrance enclosed organizelles o some organelles (i.e. DNA) re ofund in the cells of all euaryoutes and other organiells are specific to parotcular cell type (i.e. chlorospkate is an organelle found onlyin eukarytoical cells that carry out photosynthesis)
The Tree of Life (ex: bats and humans simm.)
• ex: bats forelimbs have all the same bones, joints, nerves and blood vessels found on others lims as divrse as the human arm, the forelg of a hrose, and the flipper of a whale. o All mammalian forelims are anatomical barations of a common architercuture
muscle cell experiment (master regulatory gene)
• experiment: muscle cell detmeriantion by groing myobalstc in culture and anaalyxing them suign molecules tehcniqes o in a series of expermeint they isolate different genes, causes each to be expressed ina sep. embryonic prescussor cells and then looked for differentiation into myoblast and muscle cells o they didneitifed several m"master regulatory genes" whose protein prducts commit the cells to becoming skeletal muscle o the molecular basis of determination is the expression of one or more of these master regulatory genes
Evolutionary Significance of Altered DNA Nucleotide
• faithful replication of the genome and repair of DNA damage are important for the functioning of the organism and for passing on a complete, accurate genome to the next generation • once a mismatched nucleotide pair is replicated the sequence change is permanent in the daughter molecules that has the incorrect nucleotide as well as in any subsequent copies • mutations can change the phenotype of an organism o if they occur in germs celled which give rise to gametes mutations can be passed on from generation to generation • the balance between complete fidelity of DNA replication or repair and a low mutation rate has allowed the evolution of the rich diversity of species on earth
frequency of cell division + variation of cell
• feqyency of cell dividon varies w/ the type of cell o human cells divdi freqeuntyl throuhhout light whereas liver cells mainting the ability to divide but keep it in reserve util an approaitate need arises o fully formed nerve cells and muscle cells do not divide at all in a mature human o the cell cycle difference results from regulation at molecular level
gene and strand templates
• for any given gene the same strand is sued as the template every time the gene is transcribed • for other genes on the same SNA molecule the opp. strand may be the one that always functions as the template
development in chickens and other birds
• for chickens and other brds the part of the egg that we commonly call the yolk is actually the entire egg cell o celld ivsions are litmited to a small whitsh area at the animal pole o these divsions produce a cap of cells that sort into upper and lower layers o the avaity between these two layers is the avian version of the blastocoel
Replicating the Ends of DNA Molecules
• for linear DNA the usual replication machinery cannot complete the 5' ends of daughter DNA strands o consequence of the fact that a DNA polymerase can add nucleotides only to the 3' end of a preexisting ploynucelotide o even if an Okazaki fragment can be started with an RNA primer bound to the very end of the template strand, once that primer is removed , it cannot be replaced with DNA b/c there is no 3' end available for nucleotide addition • →as a result: repeated rounds of replication produce a shorter and shorter DNA molecules with uneven or staggered ends
mitosis and cytokinesis in production of somatic cells
• from a fertilized egg mitosis and cytokeninses produced the 200 trillion somatic cells that make up the human body o the same cells continue to generate new cells to replace dead and damaged one
genes and polypeptides
• genes are typically hundred of thousands of nucleotides long-each having a specific sequence of nucleotides • each polypeptide of a protein also has monomers arranged in a particular linear order but its monomers are amino acids • nucleic acids and proteins contains info written in two different chemical languages o →getting from DNA to protein required transcription and translation
Basic Principles of Transcription and Translation
• genes provide the instructions for making specific proteins • a gene does not build a protein directly • the bridge between DNA and protein synthesis is the nucleic acid RNA
protein coding' small account for the human genome
• genome sequencing has revealed that protein coding DNA accounts for only 1.4% of the human genome and a similarily small percentage of the genomes of many multicellular eukaryotes • a very small fractions of the non-protein coding DNA consist of genes for RNAs such as ribosomal RNA and transfer RNA
heterochromatin vs. euchromatin
• heterochromatic DNA largely inaccessible to the machinery in the cell responsible for transcribing the genetic information coded in the DNA b/c of its compaction • euchromatic DNA is accessible to this machinery→the genes present in auchromatin can be transcribed
hypothesis characteristics
• hypotheses: 1. the initial observation may give rise to multiple hypotheses 2. we can never prove a hyptothesis is true
Codons: Triplets of Nucleotides
• if each kind of nucleotide base were translated into an amino acid only four amino acids could be specified, one per nucleotide base • triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids o if each arrangement of three consecutive nucleotide bases specifies an amino acid there can be 64 possible code words-more than enough for all the amino acids
chromosome of germ cells become shorter?
• if the chromosomes of germ cells became shorter in every cell cycle essential genes would eventually be missing from the gametes they produce o however this does NOT occur: an enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ cells→restoring their original length and compensating for the shortening that occurs during DNA replication
ex: E. coli
• in E. coli the process of cell divion is intiated when the DNA of the bacterial chromosome begins to replaicate at a specific place on the chrosome called the rogin of replication→prudces two orgins • as chromosome continues to replaicate one orgin movies rapidly toward opp. End of wall • while chromosome continues to replicating the cell elongates • when replication comeplte and the bacteriu, has reached about twice its intial size its plasma maberance pinches inward diving the parent E.coli cell uto twodaughter cells o each cell inherits a complete genome
E. coli and polymerase III
• in E.coli DNA polymerase III adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides, complementary to the parental DNA template strand
Anaphase in dividing animal cells
• in a dividng animal cell the nonkinetochore mictrotbles are responsible for elongating the whole cell during anaphase o nonkinetchore microtubkes from opp. Poles overla each other extensively during metaphase o during anaphase the region of overlapse is reduced as mototr proteins attach to the micritorbles wall them away from one another using energy from ATP o as microtubules push apart from one another their spindle poles are pushed apart elongating the cell o at same time the mciroutbles lengthen somewhat by the addition of tubulin subunira to their overlappin ends→microtubles continue to overlap • at end of anaphase duplicate gourps of chromosoms have arrived at opposite ends of the elongated parent cell • nucleu re-from during telephase • cytokinesis genrally beguns dyring anahse or telophase and the spindle eventually disassembly by depolymerizaition of microtubules
Metaphase chromosome
• in a mitotic chromosome the looped domains themselves coil and fold in a manner not yet fully understood o →compacting all the chromatin to produce the metaphase chromosome
bacteria
• in bacteria most genes carried on a single bacterial chromosmes that consist of a circular DNA molule and aossicated proteins
eukaryotes and bacteria
• in both eukaryotes and bacteria: multiple ribosomes translate an mRNA at the same time- a single mRNA is sued to make many copies of a polypeptide simultaneously
development in Drosphila and most other insects
• in dropshila and most other insects yolk is forund throughout the egg o early in development multiple rounds of mitosis occur without cyotkinises→no cell membrances from aroud the early nuceliu o the first several nundred nuceli spread throughout the yol and liater migreate to the otuer edge of the embro o after seceral more rounds of mitsos a plasma memrbance forms around each ucelus
Nucleosomes, or "beads on a string" (definition of nucleosome and the relation between it and histones)
• in electron micrographs unfolded chromatin is 10 nm in diameter o this chromatin resembles bead on a sting • each "bead" or chromatin is a nucleosome • nucleosome= "the basic unit of DNA packing that consists of DNA wound twice around a protein core of eight histones" • the "string" between beads is called linker DNA • the amino acid of each histone extends outward from the nucleosome • in the cell cycle: the histones leave the DNA only briefly during DNA replication o generally they do the same during transcription
o one gene-one polypeptide
• in many cases a eukaryote gene can code for a set of closely related polypeptides via a process called alternative splicing • quite a few genes code for RNA molecules that have important functions in cells even though they are never translated into a protein
chisma and metephase I
• in metaphase I homologs held together by cohesion between sister chromatid arms in regions beyond points of crossing over • crossing over and sister chromatid cohesion along the arm results in the formation of chismsa o chismaa hold homologs together as the spindle forms for the first meiotic division
yeast in siRNA
• in some yeasts siRNAs produced by he yeast cells themselves are required to re-from the heterochromatin at the centromeres→a model for how this happens shown in figure 18.15 • the siRNA system in yeast extracts with other noncoding RNAs and with chromatin-modifying enzymes to remodel chromatin structure at the centromere
the fully differentiated cell
• in the fully differentiated cell transritpion remains the principal regulatory pont for maintiaing appropriate gene expression
translation
• in the process of translation a cell :reads: a magnetic message and builds a polypeptide according • the message is a series of codons along an mRNa molecules and translator is tRNA
inherited traits determined by genes
• inherited traits are determined by genes o the trait of albinism is caused by a recessive allele of a pigmentation gene o the albino deer has a fault version of a key protein , an enzyme required for pigment synthesis, and this protein is faulty because the gene that codes for it contains incorrect information • the DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins and of RNA molecules involved in protein synthesis o proteins are the link between genotype and phenotype
The Function and Evolutionary Importance of Introns
• introns function containing sequences that regulate gene expression and many affect gene productions • one important consequence of the presence of introns in genes is that a single gene can encode more than one kind of polypeptide
exon shuffling
• introns in a gene may facilitated the evolution of new and potentially beneficial proteins as a result of a process known as exon shuffling o introns increase the probability of crossing over between the exons of alleles of a gene -providing more terrain for crossovers without interrupting coding sequence o →might result in new combinations of exons and proteins with altered structure and function o occasional mixing and matching of exons between complete different genes
Genetic Analysis of Early Development: Scientific Inquiry
• lewis surdied bizarre utant flies with developmental defects that led to extra wings or legs in the wrong place o located the mutations on the flys genetic map-connecting the develoemtan abnormalities to specific genes o supplied the first ocncerte evidence that genes somehow direct the development processes studied by embryologists o →disocered homeotic genes
The Mitotic Spindle: A Closer Look
• many of the events of mitoss depnd on the mitotic spinle which begins to form in the cytoplasm during prophase
kinases (inactivity-->activity)
• many of the kinases that dirve the cell cycle actually present at a constant conenctration in the growing cell but uch of the time they are in an inactive form • to be active such a kinase must be attached to a cyclin
many proteins undergo chemical modifications that make them functional
• many proteins undergo chemical modifications that make them functional o regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups and proteins destined for the surface of animal cells quire sugars o cell surface proteins and many others must also be transported to target destination in the cell in order to function o regulation might occur at any of the steps involved in modifying or transporting a protein
nonsteroid hormones and growth factors bind to receptors
• many signaling molecules such as nonsteroid hormones and growth factors bind to receptors on a cells surface and never actually enter the cell o such molecules can control gene expression indirectly by triggering signal transduction pathways that lead to activation of particular transcription activators or repressors o coordination regulation in such pathways is the same as for steroid hormones: genes with the same set of control elements are activated by the same chemical signals
evolution of mitosis
• mitosis evolved from simpler prokaryotic mechanism of cell reproduction • as eukaryotes w/ nuclear envelopes and larger genomes evolved the ancestrall process of binary fussion somehow gave rse to mitiss • variations oncell divison exist in different groups or orgsnims o these variant processes may be similar to mechanisms used by ancestral apsecies and thus may resemble steps in the evoltioon of mitosis from binary fission-life process
cellular system for reparing incorrectly paried nucleotides
• most cellular system for repairing incorrectly paired nucleotides use a mechanism that takes advantage of the base-paired structure of DNa o in many cases a segment of the strand containing the damage is cut out (excised) by a DNA cutting enzyme- a nuclease- and the resulting gap is then filled in with nucleotides using the undamaged strand as a template o the enzymes involved in filling the gap are a DNA polymerase and DNA ligase o →once such DNA repair system is called nucleotide excision repair
muscle cell determination
• muscle cells develop from embryonic prcusrros cells that have the ptiential to develoo into a mumber of cell types but particular conditions commit them to becoming muscle cells; o commited cells become myoblasts with determination; o myoblasts churn out large amount of muscle-specific proteins and fuse to form mature, elongated, multinucleate skeletal muscle cells
Concept 17. 5 Mutations of one or a few nucleotides can affect protein structure and function
• mutation are responsible or the huge diversity of genes found among organisms because mutations are the ultimate source of new genes
mutations and genetic diversity
• mutations are the original source of genetic diversity o these changes in an organisms DNA create the different version of genes known as alleles o reshuffling of the alleles during sexual reproduction produces the variation that results in each member of a sexually reproducing population having a unique combination of traits
ncRNA's and X chromosome inactivation
• ncRNAs are responsible for X chromosome inactivation which in most female mammals prevents expression of genes located on one of the X chromosomes o in this case: transcripts of the XIST gene located on the chromosome to be inactivated bind back to and coat that chromosomes and this binding leads to condensation of the entire chromosome into heterochromatin
chemical mutagens categories
• nucleotide analogs: "chemicals similar to normal DNA nucleotides but that pair incorrectly during DNA replication" • other chemical mutagens interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix • other mutagens cause chemical changes in bases that change their pairing properties
alteration of a single amino acid in protein
• nucleotide-pair substitutions of greatest interest are those that cause a major change in a protein • the alteration of a single amino acid in a crucial area of a protein cans significantly alter protein activity o →can lead to an improved protein or one with novel capabilities but much more often mutations are neutral or detrimental o →likely to lead to a useless or less active protein that impairs cellular function • usually missense mutations→the altered codon still does fro an amino acid and thus makes sense
second ribosome attaching to the mRNA
• once a ribosome is far enough past the start codon a sceonc ribosome can attach to the mRNA→eventually results in a number of ribosomes trailing along the mRNA
Cleavage
• once fertilization is complete the zygotes of many animal species undergo a succession of rapid cell division that characterize the celabe stage of early development • during celavr the cell cycle consists rimarily of the S and M phases, the G1 and G2 phases are essentially skipped and little or no protein synthesis occurs →result: little or no increase in mass • cleave partitions the cytoplasm of the large fertilized egg into many smaller cells called blastomeres • the frist five to seven cleave divsons produce a hollow ball of cells, the blastula, surround a flud filled cavity called the blactoceol • the pattern of ceav divisions differs among speices: the division pattern si unfirm across the embryo and in toher the pattern is asymmetric
polypeptide synthesis continuation from signal recognition particle
• polypeptide synthesis continues there and the growing polypeptide snakes across the membrane into the ER lumen via a protein pore • the signal peptide is usually removed by an enzyme the rest of the completed polypeptide is released into solution within the ER lumen • if the polypeptide is to be a membrane protein: remains partially embedded in the membrane
two types of nuclear fission (in certain unicellular eukaryotes)
• possible itnermdiate stages are suggested by two types of nuclear division found in certin unicellular eukaryotes-inoflagellates, diatoms, and some yeasts o these two does of nuclear divison thought t be causes where ancestral mechanism have reaimed relatively uncahgned over evolutionary time o in both tyes the nuclear enveloe remains intact
prokaryotic and eukarytoic genomes and DNA
• prokaryotic genome is often a single DNA molecule • eukartotic genomes usally sonsist of a number of DNA molecules
origins of replication and replication of DNA
• proteins that intuition DNA replication recognize this sequence and attach to the DNA, separating the two strands and opening up a replication "bubble" • replication of DNA then proceeds in both directions until the entire molecule is copied
Effects on mRNAs by MicroRNAs and Small Interfering RNAs
• regulation by both small and large ncRNAs is known to occur at several points in the pathways of gene expression including mRNA transation and chromatin modifications
The cell cycle clock: cyclins and cyclin-dependent kinases (rhythmic fluctuations and regulatory proteins)
• rhythmic flucntiations in the abundance and activity of cell cycle control molcues pace the sequential events of the cell cycle o these regulator moleculrs are mainly proteins of two types • protein kinases and cycles • protein kinases are enymes that activate or inactive other proteins by phosphorylating the
The Evolutionary Significance of Small ncRNAs
• small ncRNAs can regulate gene expression at multiple steps and in many ways • in general extra levels of gene regulation might allow evolution of a higher degree of complexity of from • the versitality of miRNA regulation has therefore led some bioligists to hypothesize that an increase in the number od different miRNAs specified y the genome of a given species has allow morphological complexity to increase over evolutionary time→logical to expand that discussionto include all small ncRNAs • siRNAs →miRNAs→piRNAs (found only in animals) • while there are hundreds to types of miRNAs there appear to be sixty thousand or so types of piRNAs allowing the potential for very sophisticated gene regulation by piRNAs
Types of Small-Scale Mutations (single nucleotide pair substitution and insertions or delections of nucleotide pair)
• small scale mutations with a gene's two categories o single nucleotide pair substitutions o nucleotide pair insertions or deletions • can involve one or more nucleotide pair
ncRNA-->remodeling of chromatin
• some ncRNAs act to bring about the remodeling of chromatin structure o ex: during formation of hetreochroamtin at the centromeres as studded in a species of yeast • ex: in the S phase of the cell cycle: the centromeric egions of DNA must be loosed fro chromosomal replication and then re-condensed into heterochromatin in perpeatin for mitosis
sperm binding and cortical reaction
• sperm bidning triggers a cortical reaction, the rlrease of enymes from cortical granules to the soutside of the cell o these enxyms catalyze changes in the zona pellcuida which then fucntions as the sloaw block to polypsermy
anaphase (version #1)
• structure of spindle correlates well with its function during anaphase • anaphase begins when cohesis holding together the sister chromatids of each chromosome are cleaved by an anzyme called separase o once sepeated the chromatids become full-fled chroosoms that move toward opposite end of the cell • motor proteins in the kinetochores "walk" the chromosomes along the mcrotubles which dpolymerize at their kinetochore ends afther the morot proteins have passed
Fertilization in Mammals
• terrestrial animals, including mamals, fertilize eggs internally • support cells of the developing folice sorrund the mammalian egg before and after ovusltion • a sperm must travel through this ayer of follicle cells before it reaches the zona pelldicoa→there the bidning f a sperm to a sperm recepot induces an acrosomal reaction facilitating sperm entry • the process of fertilization is sloawer in mammals than in sea urchins
Looped Domains (300-nm fibers)
• the 30-nm fiber in turn forms loops called looped domains attached to a chromosome scaffold composed of proteins • the scaffold is rich in one type of topoisomerase and H1 molecules also present
conservation of histone genes during evolution
• the apparent conservation of histone genes during evolution→reflects the important role of histones in organizing DNA within cells • these four types of histones critical to the next level of DNA packing
attachment of sister chromatids at the centromere
• the attachment is mediated by proteins bound to the centromeric DNA o other bound proteins conense the DNA; giving duplicate chromosome a narrow "waist"
cytoskeleton and cell migration
• the cytosleleton is responsible also for cell migration • during organsgeneis in vertrbates cells from the neural crest and from somites migrate to locations throughout the embryo→ells crawl within the beryo by using cytoksletal fibers to extend and restrict cellular protusions
the distinction between miRNAS and smiRNAs
• the distinction between miRNAS and smiRNAs is based on subtle differences in the structure of their precursors which in both cases are RNA molecules that are mostly double-stranded
determination
• the earliest changes that set a cell on its path to specialization are subtle onces coined determination; fere to the point at which an amebyronic cell is irreviersibly commited to becoming a particular cell type
first set of bands of cells that migrate (neural crest)
• the first set s a band of cells called the neural crest which develops along the broders where the hrual tube pinches off from the ectoderm • nral crest cells ubsequently migrate to many parts of the embryo, forming a vartt oftissues that include peripheral nerves as well as parts of the teeth and skull bones
Evolution of the Genetic Code
• the genetic code is nearly universal→shared by organisms from the simplest bacteria to the most complex plants and animals • in laboratory experiments: genes can be transcribed and translated after being transplanted from one species to another • bacteria can be programmed by the insertion of human genes to synthesize certain human proteins for medical use, such as insulin • evolutionary significance: a language shared by all living things must have been operating very early in the history of life
the genetic instructions for a polypeptide chain
• the genetic instructions for a polypeptide chain are written in the DNA as a series of non-overlapping, three-nucleotide words o the series of words in a gene is transcribed into a complementary series of non-overlapping, three- nucleotide words un mRNA→translated into a chain of amino acids
Ribosome Association and Initiation of Translation
• the initiation stage of translation brings together mRMA, a tRNA bearing the first amino acid of the polypetide and the two suits of a ribosome 1. a small ribosomal subunit binds to both mRNa and a specific initiator tRNA which carries the amino acid methionine
genome in most bacteria (proteins to cause chromosome to coil and supercoil)
• the main component of the genome in most bacteria: one double-stranded circular DNA molecule that is associated with a small amount of protein o this bacterial chromosome is very different from a eukaryotic chromosome • within a bacterium certain proteins cause the chromosome to coil and "supercoil" densely packing it so that if fills only part of the cell
the process of cellular signaling in development
• the moelcules conveing these signals within the target cell are cell0srucace receptiors and other signaling pathways proteins • the signaling mcluels send a cell down a specific developmental path by causing changes in its gene expression • interactions between embryonic cells help include differentiation into the many specialized cell types making up a new organism
movement of bacterial chromosomes
• the movement of bacterial chromosms is reminiscent of the poleward ovemnts of the centromere regions of eukaryotic chromsoms during anaphase of mitoss o but bacteria don't have visble mitotic spindles or even microtubules o the two origins of replication origins of replicagion end up at top. Ends of the cell in some other very soefuc location
30 nm fiber
• the next level of packing results from interactions between the histone tails of one nucleosome and the linker DNA and nucleosomes on either side • the fifth histone, H1, is involved at this level • these interactions cause the extended 10-nm fiber to coil or fold→a chromatin fiber roughly 30 nm in thickness
Completing and Targeting the Functional Protein
• the process of translation often not sufficient to make a functional protein
Random Fertilization
• the random nature of fertilization adds to the genetic variation arising from meiosis • in humans: each male and female gamete represents one of about 8.4 million possible chromosome combinations due to independent assortment • the fusion of a male gamete with a female gamete during fertilization will produce a zygote with any of about 70 trillion diploid combinations o if we factor in the variation brought about by crossing over the possibilities are truly astronomical
origins of replication
• the replication of a chromosome begins at particular sets called origins of replication "short stretches of DNA having a specific sequence of nucleotides • a eukaryotic chromosome may have hundred or even a few thousand replication origins o multiple replication bubbles form and eventually fuse→speeding up the copying of the very long DNA molecules
convergent extension
• the sytokselton also direct a morhogenetic movement called convergent extnension : "a rearrangement that causes a sheet of cells to become narrower whie it becomes longer" o the cells elongate with their ends pointing tin the direction they will move and they then widege between ach other to from fewr coli,s of cells o also important in other setting such as involution in the frog gastrula: convergent exntesion changes the gastrulating embro from a spherical shape to the rounded rectangle shape
concept 12.3 the eukaryotic cell cycle is regulated by a molecular control system
• the timing and rate of cell vision in different parts of a plant or animal are curical to normal growth, development and maintenece
Antiparallel Elongation
• the two ends of a DNA strand are different, giving each strand directionality, like a one-way street • the two strands of DNA in a double helix are antiparallel-meaning that they are oriented in opposite direction to each other o two ne strands formed during DNa replication must be antipareallel to their template strands
sister chromatids-->seperate chromosomes
• the two sister chromatids of each duplicated chromosome serpaete and move into two new nuclei→one forming at each end of the cell • once the sister chromatids separate they are no longer called sister chromatids but are considered individual chromosomes o →this step essentially doubles the number of chromosomes in the cell o →each new nucleus receives a collection of chromsomes identical to that of the parent cell
complementary DNA strands
• the two strands are complementary: each stores the information necessary to reconstruct the other • when a cell occupies a DNA molecule each strand serves as a template for ordering nucleotides into a new, complementary strand o nucleotides line up along the template strand according to the base-pairing rules and are linked to form the new strands o →two strands of the double helix, each an exact replica of the "parental" molecule
translation initiation complex (components)
• the unition of mRNa and initiation tRNA and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit completing the translation initiation complex
topoisomerase
• the untwisting of the double helix causes tighter twisting and strain ahead of the replication fork • topoisomerase helps relieve this strain by breaking swiveling and rejoining DNA strands "an enzyme in which helps relieve the strain caused by the untwisting of the double helix by breaking swiveling and rejoining DNA strands"
unwound sections of parental DNA strands= template for synthesis
• the unwound sections of parental DNA strands are now available to serve as templates for the synthesis of new complementary DNA strands • the enzymes that synthesize DNA cannot initiate the synthesis of a plynucleiotide->they can only add DNA nucleotides to the end of an already existing chain that is base-paired with the template strand • the initial nucleotide chain is actually a short stretch of RNA not DNA
The Genetic Code
• there are only four nucleotide bases to specify 20 amino acids
redundancy in genetic code but no ambiguity
• there is a redundancy in the genetic code but no ambiguity o EX: GAA AND GAG both specify for glutamic acid but neither of them ever species any other amino acid • Codons that are synonymous for a particular amino acid differ only in the third nucleotide base of the triplet
Regulation of Cleave
• thr single nucleus in a newly fertilized egg has too little DNA to produce the amount of messenger RNA required to meet the cells need for new protiens • instead intial development is carried out by RNA and proteins deposited in the egg during oofeneis • after cleaveage the egg cytoplasm has been divided mong the many blastomeres, each with its own nulcue o b/c each blastomere is much smaller than the entire egg, its nucleus can make aenough RNA to program the cells metabolism and further development
testing hypothesis
• to test hypothesis: scientists injucted pure biocid mRNa into various regions of early embryos; the prtein that resulted from its translation caused anterior strucutres to form at the injection stites o →led to the identification of a specific protein required for some of the earlist steps in pattern formation->helped us understand how different regions of the egg can give rise to cells that go down differential developmental pathways o in crease our understanding of the mothers cirticual role in the intial phases of embryonic development o the principes that a gradient of morphoenges can determine polarity and position has rpoved t be a key developmental concept for a numer of species
Mechanisms of Post-Transcriptional Regulation
• transcription alone does not constitute gene expression • the expression of a protein coding gene is ultimately measured by the amount of functional proteins a cell make and much happens between the synthesis of the RNA transcript and the activity of the protein in the cell • many regulatory mechanisms operate at the various stages after transcription o these mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes without altering its transcription patterns
Building a Polypeptide (translation three stages)
• translations three stages: initiation, elongation and termination o all three stages require protein :factors: that aid in the translation process o for certain aspects of chain initiation and elongation energy is also required; provided by the hydrolysis of guanosine triphosplate
fusion of two cells in different stages
• two cells in different pahses of the cell cycle were fused to from a single cell with two nucle o if one fo the original cellsw as in the s pahse and other in g1, the g1 nuclues immediately entred the s phase as though stimulated by signling molecules present in the cytoplasm of the fist cell o if a cell undergoing itios (m phase) was fused with another cell in any
main forms of cells
• two main forms of cells: prokaryotic and eukaryotic o prokaryotic: bacteria and archaea o eukaryotic: all other forms of life, including plants and animals
Gasturlation in Humans
• unlike the large hyolk eggs of many verebrates human eggs are wuite small, storing little in the way of food resrves • fertilization takes palces in the oviduct and development begins while the embro compeltes it journey down the oviduct to the uterus
Making Multiple Polypeptides in Bacteria and Eukaryotes (general)
• when a polypeptide is required in a cell the ened is for many copies not just one • a single ribosome can make an average polypeptide in less than a minute
distribution of chromosoms during eukarytoitic cell divison
• when cell not diving each chromosome is in the form of a long think chromatic fiber • after dnas replication howveer the chromosoms condenses as a part of cell division • each chromatin fiber becomes denselt coild and foiled--?making the chjromsoms much shorter • each duplicated chromosome has two sister chromatids
Chromosome Alignment on Metaphase Plate
• when one of a chromsomes kinetochores is captured by microtibles the chromosome begsin to move toward the pole from which those microtubules extend o this movement is chaecked as soon as microtubules from the opp. Pole attach to the kinetochore on the other chromatid • the chromosome mvoes first in one direction then in the other back and forth until finally settle midway between the two end of the cell • at mtahase the centromeres of all duplicated chromosomes are on a plane midway between the spindles to poles
birds, other repitlces, many fishes and insects
• yolk is most plentiful and has its most prodounded effect on cleave in the eggs of brd, other repitles, many fishes and isnetcts o in these animals the volume of yolk is so great that cleage furors cannotpas s through it and only the regions of the egg lacking yolk undergoes cleavage
The Stages of Meiosis (Meiosis Goal)
For a single pair of homologous chromosomes in a diploid cell: both member of the pair are duplicated and the copies sorted into four haploid daughter cells
• four types of histones most common in chromatin
G2A,H2B,H3, H4
gene with heterochromatin
Genes with heterochromatin which is highly condensed are usually not expressed
Cytokinesis in animal cells
In animal cells cytokinesis occurs by a process known as cleavage --> the first sign is the appearance of a cleavage furrow
Gametes
In animals and plants reproductive cells called gametes are the vehicles that transmit genes from one generation to the next "the reproductive cells in animals and plants that transmit genes from one generation to the next" o During fertilization male and female gametes (sperm and eggs) units→pass on genes of both parents to their offspring
Sets of Chromosomes in Human cells
In humans each somatic cell has 46 chromosomes There are two chromosomes of each of 23 types o This becomes clear when mages of the chromosms are arranged in pairs, starting with the longest chromoms
Synthesis of an RNA Transcript Three stages of transcription
Initiation, Elongation, Termination
inversions
Inversions (reversed sequences of gene loci) can repress genetic recombination, since crossing over makes incomplete, usually nonfunctional, chromosomes
What determines or generates genetic variation?
Key: the behavior of chromosomes during the sexual life cycle
image of DNA replication
LOOK ON WORD DOCUMENT
The Variety of Sexual Life Cycles
Meiosis and fertilization is common to all organisms that reproduce sexually BUT the timing of these two events in the life cycle varies, depending on the species
Meiosis (double division)
Meiosis: single duplication of chromosomes is followed by not one but two consecutive cell divisions called meiosis I and meiosis II o The two divisions result in four daughter cells -each with only half as many chromosomes as the parent cell
natural selection and diversity
Natural slection could cause an ancestral specifies to give rise to two or more descenet species; if one pop fragmented into several subpops isolated in different enviroments
difference in division between cancer and normal cells
Nearly all normal mammalian cells grown in culture and divide only about 20 to 50 tmes before they age and die Cancer cells evade the normal controls that trigger a cell to undergo apoptosis when something is wrong
protein complex
Once activated the compex sets off a chain of molecular events that activates the enzyme separase (cleabes the cohesis) allowing th sister chromatids to seprate o Mechanism ensures that daughter cells do not end up w/missing or extra chromosms
reqs. for transcribing
Once appropriate transcription factors attached to the promoter DNA and the polymerase bound in correct orientation the enzymes unwinds the two DNA strands and begins transcribing the template strand at start point
Comparison of Asexual and Sexual Reproduction
Only organisms that reproduce asexually have offspring that are exact genetic copies of themselves
human genome
Our genome consists of the genes and other DNA that make up the chromosome we inherited from our parents
Concept 13.1 : Offspring acquire genes from parents by inheriting chromosomes Inheritance of genes
Parent endow their offspring with coded information in the form of hereditary units called genes
how do cells acquire different fates?
Particular tissues and often cells within a tissue differ from one another by expressinf distinct sets of genes from their shared genome
Independent Assortment of Chromosomes
Random orientation of pairs of homologous chromosomes at metaphase of meiosis I
cell-cell adhesion (cadherins)
Some of the proteins implicated in cell-cell adhesion, and in changes of adhesion patterns, are called cadherins, which reversibly adhere cells based on the presence or absence of calcium ions.
gastrulation as a consequence of cell-cell adhesion
The cell movements during gastrulation, which rearrange a confluent assemblage of cells into a layer of external cells (ectoderm), a tube of interior cells (endoderm), and clusters of intermediate cells (mesoderm), are a consequence of changes in cell-cell adhesion.
organ system
The complex organization of all organs within a specifies
fluctuating activities of different cyclin-CDK
The flucntiating acticvities od fiferent cyclin-Cdk complexes are of major importance in control all the stages of the cell cycle and give the go-ahead single at some checkpints as well o Cell bevharior sat the G1 checkpont also regulated by activity of cyclin-Cdk prtein compelxes
beginning of human life cycle
The human life cycle beings when a haploid sperm from the father fuses with a haploid egg from the mother
Ribozymes
The idea of a catalytic role of the RNA in the splicesome arose from the discovery of ribozymes
eukaryotic RNA and polymerase II interaction
The interaction between eukaryotic RNA polymerase II and transcription factors is an ex of the importance of protein-protein interactions in controlling eukaryotic transcription
genes and base sequences
The linear sequence of the four bases can be varied in countless ways and each gene has a unique base sequence
location of gene promoter
The location of a genes promoter can affect whether the gene is transcribed
Concept 16.2 Many proteins work together in DNA replication and repair
The relationship between structure and function is manifest in the double helix
homolog
The two chromosomes of a homolgous pair are individual chromosomes that were inherited from different parents Homologs may have different versions of genes, each called an allele, at corresponding loci Homologs not associated with one another in any obvious way except during meiosis
Gene Duplication: Mechanism
Unequal Sister Chromatid Exhachange Unequal Crossing over
Improper crossing over can lead to various types of chromosomal mutations
Unequal exchanges: deletions, gene duplications Nonparallel lineup: inversions Non-homologous chromosomes: translocations
Genome
a cells endwoemnt of DNA
nucleotide excision repair
a cellular system for repairing incorrectly paired nucleotides in which a segment of the strand containing the damage is cut out (excised) by a DNA cutting enzyme- a nuclease- and the resulting gap is then filled in with nucleotides using the undamaged strand as a template
silent mutation
a change in a nucleotide pair in which transforms one codon into another that is translated into the same amino acid→have little effect on the protein" o new amino acid may have properties similar to those of the amino acid it replaces or it may be in a region of the protein where the exact sequence of amino acids is not essential to the proteins function
molecule
a chemical structure consisting of two or more units called atoms
Transcription factors
a collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription"
cell cycle control system
a cyclically operating set of molecules in the cell that both triggers and coordinates key events in the cell cycle" o the cell cycle proceeds on its own according to a built in clock but the cell cycle is regulated at certain checkpints by bother inetnal and external singlas that stop or restart the process
eukaryotic replication
a eukaryotic chromosome may have hundred or even a few thousand replication origins o multiple replication bubbles form and eventually fuse→speeding up the copying of the very long DNA molecules • eukaryotic DNA replication proceeds in both directions from each origin • at each end of a replication bubble is a replication fork
Alternative RNA splicing
a form of regulation at the RNA processing level in which different mRNA molecules are produced from the same primary transcript depending on which RNA segments are treated as exons and which as introns" • Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequence • Other genes code for many more possible products • Alternative RNA spicing can significantly expand the repertoire of a eukaryotic genome o Alternative splicing was proposed as one explanation for the surprisingly low number of human genes counted when the human genome was sequenced o 75-100% of human genes that have multiple exons probably undergo alternative splicing →the extent of alternative splicing greatly multiplies the number of possible human proteins
gene and primary structure primary structure and shape
a gene determine primary structure and primary structure in turn determines shape
maternal affect gene
a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offpsrings own genetoype
Locus
a genes specific location along the length of a chromosome"
one gene-one enzyme hypothesis
a hypothesis that that states that the function of a gene is to dictated the production of a specific enzyme"
splicesome
a large complex made of proteins and small RNA that remove introns in pre-mRNA" o Binds to several short nucleotide sequences along an intron o The intron then released and the splicesome joins together the two exons that flanked the intron o Small RNA in the splicesome also catalyzed the splicing reaction
negative feedback
a loop in which the reponse reduces the intial stimulius; the output of the process negatively regulates that process
massive study of the entire human genome and its conclusions
a massive study of the entire human genome completed in 2012 showed that roughly 75% of the genome is transcribed at some point in any given cell o introns account for only a fraction of this transcribed and nontranscribedRNA o →suggest that a significant amount of the genome may be transcribed into non-protein-coding RNA—also called noncoding RNAs or ncRNAs—including a variety of small RNA
5' cap
a modified form of a guanine nucleotides added onto the 5' end after transcription of the first 20-40 nucleotides"
missense mutations
a mutaiton in which the altered codon still does fro an amino acid and thus makes sense
Density-dependent inhibit
a phenomen in which crowded cells stop dividing
Genomic imprint
a process in which "methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development"
induction
a process in which a group of cells or tissues influence the development of another group through close-range interactions
cyclin
a protein that gets its name from its cyclically fluctuating concentration in the cell
signal-recognition particle
a protein-RNA complex that recognizes signal peptides as it emerges from the ribosome" o function as an escort that brings the ribosome to a receptor protein built into the ER membrane o the receptor is part of a multiprotein trnlocation complex • other kinds of signal peptides are used to target polypeptide to mitochondria chloroplasts, the interia of the nucleus, and other organelles that are not part of the endomembrane system
aster
a radial array of short microtubules
centromere
a region of the chromosomal DNA where the chromatid is attached most colselt ro its sister chromatid
notchord
a rod that extends along the dorsal side of the chordate embryo
experiment
a scientific test, carried out inder conditrolled conditions
gastrulation
a set of cells at or near the surface of the blastula moves to an interior location, cell layers are established and a primitive digestive tube is formed
cleavage furrow
a shallow groove in the cell surface near the old metaphase plate
acrosome
a specialized vesile at the tip of the sperm
model organism
a species that is easy to grow in the lab and lends itself particularily well to the questions being invesitngated; can be viewed as a model for understanding the biology of other specieses and deiseas o Ex: the fruit fly Drosophila melanogaster→teach us a lot about howgenes work in other species, even humans
centrosome
a subcellular region contining material that functions throughout the cell cycle to organie the cells microtubules • a pair of centrioles is located at the center of the centrosome but ot essential for cell division o if centrails destroyed a spindle neveretheless forms during mitosis
hypothesis
a tentative answer to a well framed question; suually a rational account for a set of observation, based on the avubalbe data and guided by inductive reasoning o must lea to predictons that can be tested by making additional observations or by perfroming experiemnts
bicoid
a term meaning "two tailed"
Synaptonemal complex
a zipper-like structure that holds one homology tightly to the other
signal peptide
a" peptide in which targets the protein to the ER" o made up of about 20 amino acids at or near the leading end of the polypeptide and is recognized as it emerges from the ribosomes by a protein RNA complex called a signal-recognition particle
chemical modifications of histones
affect the state of chromatin condensation and also have multiple effects on gene activity
Initiation
after RNA polymerase binds to the promoter, the DNA strands unwind strand the polymerase initiations RNA synthesis at the start point on the template strand
Most Fungi and Some Protists: Life Cycle
after gametes fuse and form a diploid zygote meiosis occurs without a multicellular diploid offspring developing→meiosis reduces not gametes but haploid cells that then divide by mitosis →rise to either unicellular descendent of a haploid multicellular adult organism→the haploid organism carries out further mitoses→producing cell that develop into gametes
somatic cells
all body cells excpte the reproductive cells o each contain 46 chromosomes, made up of two sets of 23, one set inherited from each parent
seed
an embryo surrounded by a store of food and a protective coat
positive feedback
an end product speed up its own production (i.e. the clotting of yoyr blood in repsnse to inhury; when blood vessel damaged, strucutes in blood called platelets begin to aggregate as site→chemical releated by platelets attract more laetlests)
seperase
an enzyme that cleave the cohesions holding together the sister chromatids of each chromosome-->allow them to become full-fled chromosomes
RNA polymerase
an enzyme that pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand→elongating the RNA polynucleotide" • RNA polymerase can assemble a polynucleotide only in its 5'→3'direction • RNA polymerase able to start a chain from scratch; they don't need a primer • Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends
organism
an individual living thing
E site
area in which the discharged tRNA leave the ribosome"
Molecules: Interactons within Organisms:
at lower levels of orgnaizaiton the interactions between componets that make up living organisms are cieucla ot smooth operaitons
bilateral versus radial symmetry
bilaterial:Animals with bilateral symmetry have a "head" and "tail" (anterior vs. posterior), front and back (dorsal vs. ventral), and right and left sides. All true animals, except those with radial symmetry, are bilaterally symmetrical. radial symmetry: a basic body plan in which the organism can be divided into similar halves by passing a plane at any angle along a central axis, characteristic of sessile and bottom-dwelling animals, as the sea anemone and starfish.
o An activation domain
binds other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in an enhanced transcription of a given gene. " o A transcription factor can have one or more of either type of domain
eukaryotes vs. prokaryotes in their ability to transcribe multiple mRNAs from the same gene
both eukaryotes and bacteria can transcribe multiple mRNAs from the same gene o the coordination of the two processes—transcription and translation—differ in bacteria and eukaryotes o most important difference arises from the bacterial cells lack of compartmental organization→a bacterial cell ensures a streamlined operation by coupling the two processes + in the absence of a nucleus it can simultaneously transcribe and translate the same gene and the newly made protein can quickly diffuse to its site of function o eukaryotic cell: its nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing
metaphase and microtubules from asters
by metpahse the microtubules from the asters have also grown and are in contact with the plasma mebrance
cancerous cells and short telomeres
cells from large tumors usually have unusually short telomeres→makes sense as cells that have undergone many cell divisions o telomerase activity is abnormally high in cancerous somatic cells o for several years researchers have studied inhibition of telomerase as possible cancer therapy
Sex Chromosomes
chromosome responsible for hereditary traits due to sexual reproduction, X and Y chromosomes"
anaphase (version #2)
chromosomes are "reeled in" by motor proteins at the spindle poles and that the microtubules depolyerixe after they pass by these motor proteins
crossing over: metaphase II
chromosomes that contain one or more recombinant chromatids can be oriented in two alternative, non-equivalent ways w/ respect to other chromosomes o the different possible arrangements of non-identical chromatids during meiosis II further increase the number of genetic types of daughter cells that can result from meiosis
ecosystem
concists of all the living things in a particular aea, along with all nonling componenets of the environment in which kife interacts
tissue
consists of a group of cells that work together, performing a speciailied function, to achieve a specific or targeted goal
biosphere
consists of all life on earth and all pleaces where life exists
population
consists of all the individuals of a specified living within the bounds of a pseicified area
mitotic spindle
consists of fibers made of microtubules and associated proteins" o while mititoic spind assembles other micrituble of the cytoskeleton partially disassemble →privde material used to construct the spindle o the spindle microtubules elongated (polymerize) by inciprateing more subunits of the protein tubulin and shorten (depolymerize) by losing subunits in animal cells the assembly of spindle microtubules start at the centrosome
The Cytoskeleton in Morphogenesis
development • at the onset of neural tube formation microtbeles ortiented from dorsal to ventral in a sheet of ectodermal cells help lengthen the cells along that axis • at the dorsal end of each cell is a bundle of actin filament ortiented crosswise o these can failament contract giving the cells a swide shape that bends the ecodterm layer inward • simmilair changes occur at the hinge egions were the nrual tube is pinching off from the ectoderm
allantois
diposes of wastes in the reptilian egg is cinropted into the umbilical cord in mammals o →there it forms fblood vessles that transport ocygen and nturitents from the placenta to the embryo and rid the embryo of carbon dioixd and niteogenous wastes
domains
discrete structural and functional regions within the modular architecture of proteins" o one domain of an enzyme might include the active site while another might allow the enzyme to bind to a cellular membrane o different exons usually code for the different domains of a protein
emergent properties
due o the arrangement and interactions of parts as complexity increases o not unqiue to life
kinetochore microtubules
during prometphase some of the spindle micritobles attach to the kinetochores
yolk sac
encloses yol in the eggs f repitles and in mammals is a site of early formation of blood cells which later mgrate into the embryo proper
Slow block to polyspermy
established by vesicles that lie just beneath the egg plasma membrane, in the rim of cytoplasm known as the cortex o Within secons after a sperm binds to the egg these vesilec—cortucal granules—fuse with the egg plasma membrance o Contents of vesilces are released into the space beteween the plasma membrance and the surround vitelline layer- a structure formed by thee eggs extracellular matrix o Enzymes and other macromolecules from the granules then trigger a cotical reaction whick lifts the vitelline layer away from the egg and hardens the layer into a protetive fertilization envelope o Additional enxymes clip fff ans release the exnternal protions of the remaining receptor proteins along with any attached sperm
Termination
eventually the RNA transcript is released and the polymerase detaches from the DNA
Dropsphila research for segmentation development
ex[psing flies to a mtagent chemical that affected the flies' gamtes; mated the mutagenixed flies and then scanned their descenedents for dead embryos or larva with abnormal segementation or other defects o ex: to find genes that might set up anterior-posterior axis they looked for embryos or larvae with absnormal ends such as two ehads or two tails, predicating that such abnormalities would arise form muations in maternal genes required for correctly setting up the offpsirns head or tail end
Plants and Some Species of Algae: Life Cycle (alternation of generations) (sporophyte vs. gametophyte)
exhibit the life cycle called alternation of generations; includes both diploid and haploid stages ---multicellular; the multicellular diploid stage is called the sporophyte, meiosis in the sporyphyte produces haploid cells called spores→a haploid spore doesn't fuse with another cell but divides mitotically →a multicellular haploid staged called gametophyte→give rise to gametes by mitosis→fusion of two haploid gametes at fertilization→diploid zygote--?the next sporophyte generation • The sporophyte generation produces a gametophyte at its offspring and the gametophyte generation produces the next sporophyte generation
cilia
extensions of cells that function in locomotion. They occur in ekaryotes as diverse as Paramecium and humans
ECM
extracellular matric: the meshwork of secteted glycoportiens and other macromolecules lyingoutside the plasma membrance of cells • the ECM helps to duide cells in many tpes of movmeents sch as migration of idnvidual cells sand shape changes of cell sheets • cells that line migration pathways regulat movement of migrating cells by secreting specific ,molvuleces into the ECM
protein-protein interacts
facilitate the efficient of this complex o Ex: by interacting with other proteins at the fork, primase apparently acts as a molecular brake, slowing progress of the replication fork and coordinating the placements of primers and the rates of replication on the leading and laggings strands
Human and Most Other Animals: Life Cycle
gametes are the only haploid cells: meiosis occurs in germ cell during the production of gametes which undergo no further cell division prior to fertilization→post fertilization the diploid zygote divides by mitosis→a multicellular organism that is diploid
hometotic genes
genes that control pattern formation in the late embryo, larva and adult
moorphogen gradient hyptheiss
grandients of susbtances called mropgones establish an embryos axes and other featurs of its form
germ layers
group of cells in an embryo that interact with each other as the embryo develops and contribute to the formation of all organs and tissues.
Dependent Variable
hat which is measured
Eukaryotic Synthesis
he situation in eukaryotes is ore complicated than E.coli with at least 11 different DNA polymerases discovered so far, though the general principles are the same
P site
hold the tRNA carrying the growing polypeptidechain"
A site
hold the tRNA carrying the next amino acid to be added to the chain"
E. Coli DNA Synthesis
in E.coli: two polymerase appear to play the major roles in DNA replication: DNA polymerase II and DNA polymerase I
free and bound ribosomes
in electron micrograph of eukaryotic cells active in protein synthesis two populations of ribosomes are evident: free and bound
eukaryote initiation
in eukaryotes: the small subunit with the initiator tRNA already bound binds to the 5' cap of the mRNA and then moves downstream along the mRNA until it reaches the start codon
humans and crossing over events
in humans an average of one to three crossover events occur per chromosome pair depending on the size of the chromosomes and the position of their centromeres
mitotic (M) phase
includes both mitosis and cytokinesis and is sually the shortest part of cell o alternates with interphase
meroblastic:
incolv,plete cleave of a yolk-rich egg
chorian
is the site of gas exchange and the fluid within the amnion physically protects the developing embryo
sister chromatids
joined cipoues of the orginal choromsome
cyclin-dependent kinases
kinases that must be attached to acyclin to be active o the activity of a cdk rises and falls with changes in the concentral of its cyclin partner o the flunctiating activity of MPF (the cyclin-cdk complex) corresponds to the peaks of the cyclin concentration o the cyclin level risis during the S and g2 phases and then falls abruptly during M ohasr
prokaryotic cell
lacks a nucleus or other membrance enclosed organielles
mesoderm
layer that forms between the ectoderm and endoderm
cell
lifes funcdemntal unit of structures and fuction; some rganisms have single cells (performs all function of life) or multiple cells( divisin of labor for operation)
deductive reasoning
logic that goes from the general to the specific; takes the from of predictions of results that will be found if a particular hypothesis is correct... "if...then" logic
Concept 17.2: Transcription is the DNA-directed synthesis of RNA: A closer look Molecular Components of Transcription
mRNA is transcribed from the template strand of a gene
DNA Structure
made up of two long chains arranged in a double heliz each made up of four chemical bulding blocks called neucotides (ATCG)
maternal mRNas and development
maternal mRNas are crucial during development of many species
Cytoplasmic determinants
maternal susbtances in the egg that influence the course of early development
microtubules that do not attach to kinectocores movement
micrtubles that do not attach to kinetchors have elongated and by methapjse overlap and interact w/ other nonkinetcochore microtubes from the opp. Pole of the spinle
DNA polymerase reqs.
most DNA polymerases require a primer and a DNA template strand, along which complementary DNA nucleotides are line up
prokaryotes method for not shortening
most prokaryotes have a circular chromosomes w/no ends→shortening of DNA does not occur
Theory
much broader than a hypothesis, can spin of many new specific hypothesis and is supported by a much greater bod of evidence
spontaneous mutations
mutations in which if not checked by DNA proofreading an incorrect base is used as a template in the next round of replication"
embryonic lethals
mutations with phenotypes causing death and the embryonic or larval stage
• why did this adaption appear in the volutinary history of repitlces and mamals but not other vertebrates such as fishes and amphibians?
o All vertebrate embryos rwuire an aqueous environemt for their development o The mebryos of fishes and amphibaisn usually develop in the surround sea or pond and need no specialized water-filled enclosure o Hweve the extenseive colonization of land by vertebrates was possible only after the evolution of strucutres that would allow reproduction in dry environment o Two such strcutres exist twday: the shelled egg of brids and other respitles as well as mammals (the montomeres) and the uterus of mastrupial and eutherian mammals • Inside the shell or uterus the mebryos of these animal are surrounded by fluid within a sac formed by one of the extramebrtonic mebrance, the annion • Mammals and repitlces are therefore called amniotes
• What generates the first differences among cells in an early embryo? And what controls the differnetiaion of all the various cell yypues as develiment proceeds?
o Answer: specific genes expressed in any particular cells of a developing organism determines its path; two sources of ino tell a cell which genes to express at any given time during embryonic development
The Acrosomal Reaciton
o Begins with the discharge of hydrolytic enzymes from the acrosome o These enzymes partially digest the jelly coat enabling a sperm strcutred ca;;ed the acrosomal process to eleonate and penetrate the coat o Protein molcules on the tip of the exnteded acrosomal process bind to specific repocetproteins that just out from the plasman mebrance of the egg→really important for sear urnchances because that water into which sperm and eggs are released may contain gametes of other speciies o The recongtion event etween the sperm and egg triggers fusion of their plasma mebrace • Sperm nucleus enters the egg cypolasm as ion channels open in the eggs plasa memrbance • Sodium ions diffuse into the egg and cause depolication
culture cells (division)
o Cultures cells normally divide until they form a single layer of cells on the inner surface of the culture flask at which point the cells stop dividing o If some cells are removed those bordering the open space begin diving again and continue until the vacancy is filled o The biding of a cell-surfaxe protein to its counterpoart on an adjoin cell sends a cell division inhibiting signal to both cells, preventing them from moving foeard in the cell ceycle even ine presence of growth factors
incorrectly paired or altered nucleotides c
o DNA molecules constantly subjected to potentially harmful chemical and physical agents o DNA bases often undergo spontaneous chemical changes under normal cellular conditions o →these two changes in DNA are usually corrected before they become mutations perpetuated through successive replications
maternal mRNas and development in Drosphila
o Dropshia: graidnets of specific proteins encoded by matnerla mRNAs not only detrmind the posterior and anterior ends but also establish the dorsal-betanl axis; as the embryo greows it reaches a ppint when the embryonic program of ene expression takes over, and the maternal mRNAs must be destroyed; later position info encoded by embryos genes established a specific number of correctly oriented segements and triggers the formation of each segeents characteristics strucutres
Modification to the chromatin can be reversed
o Ex: DNA methylation patterns are largely erased and reestablished during gamete formation
Bdelloid rotifer (example of species that can create genetic diversity w/out sexual reproduction)
o Has mechanisms other than sexual reproduction for generating genetic diversity o They live in environment that can dry up for long periods of time during which they can enter a state of suspended animation o →their cells membrane may crack in places, allowing entry of DNA from other totifers→increased genetic diversity
• How does the eukaryotic cell deal with a group o genes of related function that need to be turned on or off at the same time?
o In bacteria: such coordinately controlled genes are often clustered into an operon which is regulated by a single promoter and transcribed into a single mRNA molecule o →thus the genes are expressed together and the encoded proteins are produced conceurrently o with a few exceptions operons that work in this way have not been found in eukaryotic cells
McDowalls Finding
o Indicate latitudinal difference in worldwide distribution of anadromous and catadromous fish→anadromy more common in temperate latitude and catadromy in the tropics o Hypothesis: evolution theory provided with information on a substantial fitness benefit to a diadromous migrant and geographical distribution of diadromy
RNA vs. DNA
o It contains ribose instead of deoxyribose as its sugar and has the nitrogenous base uracil rather than thymine o An RNA molecule usually consist of a single strand • in DNA and RNA the monomers are the four types of nucleotides which differ in their nitrogenous bases
Growth Rate Increase
o Juvenile anadromous pacific salmon: experience a 10 to 50% increase in their daily growth trate during first week of ocean life o w/in seven salmonoid species: only significant difference was that individuals diadromous populations produced more eggs than those in nondiadromous populations as consequence of body size o experimental increase in availability of freshwater food→decrease incidence of anadromous migration by artic char o Conclusion: access to food resource for body growth is an important benefit for diadromy
G1 checkpoint (restriction point):
o Most important o If a cell receives a go-ahad signal at the G1 checkpoiunt it will usually complete the G1, S and G2 and M phases and divide o If a cell does not receive the go-ahead signal at that point it may exit the cycle switching into a nodniding state called the G0pahse • Most cells of the human body actually in the G0 phase
what determine a free or bound ribosome?
o Polypeptide synthesis always begin in the cytosal as a free ribosome starts to translate an mRNA molecule o →the process continues to completion unless the growing polypeptide itself cues the ribosomes to attach to the ER o the polypeptide of proteins destined for the endomembrane system for secretion are marked by a signal peptide
The two chromsoms of a pair have...
o The same length o Centromere position o Staining pattern
Hershey and Chase experiment:
o Used a radioactive isotope of sulfur to tag protein in one batch of T2 and a radioactive isotope of phosphorus to tag DNA in a second batch o b/c protein (NOT DNA) contain sulfur radioactive sulfur atoms were incorporated into the protein of the phage o the atoms of radioactive phosphorus labeled on the DNA b/c nearly all the phages phosphorous is in the phages DNA o separate samples of nonradioactive E. coli cells were infected with the protein-labeled and DNA labeled batches of T2 o tested the two samples shortly after the onset of infection to see which types of molecule (DNA or protein) had entered the bacterial cells and would therefore be capable of reprogramming them o →phage DNA entered the host cells but the phage protein did not o →when these bacteria were returned to a culture medium and the infection ran its course the E.coli released phages that contained some radioactive phosphorous
Three properties of RNA enable some RNA molecules to function as enzymes
o b/c RNA is single-stranded a region of an RNA molecule may base-pair in an antiparallel arrangement with a complementary region elsewhere in the same molecules→3-D structure o lice certain amino acids in an enzymatic protein some of the bases in RNA contain functional groups that can participate in catalyses o the ability of RNA to hydrogen-bond with other nucleic acid molecules adds a specificity to its catalytic activity • complementary base paring between the RNA of the splicesome and the RNA of a primary RNA transcript precisely locates the region where the ribozyme catalyzes splicing
• one gene-one enzyme hypothesis
o biochemists accumulated much evidence that cells synthesize and degrade most organize molecules via metabolic pathways in which each chemical reaction in a sequence it catalyzed by a specific enzyme
ribosome
o consist of a large subunit and a small subunit each made up of proteins and one or more ribosomal RNA o in eukaryotes: the subunits are made in the nucleolus→ribosomal RNA genes are transcribed and then RNA is processed and assembled with proteins imported from the cytoplasm→completed ribosomal units are then exported via nuclear pores to the cytoplasm o in both bacteria and eukaryotes a large and a small subunit join to form a functioning ribosome only when attached to an mRNA molecule
one gene-one protein
o doesn't work either because many proteins are constructed from two or more different polypeptide chains and each polypeptide is specified by its own gene
independent assortment (daughter cell + combinations)
o each daughter cell represents one outcome of all possible combinations of maternal and paternal chromosomes • the number of combinations possible for daughter cells formed by meiosis of a diploid cell with two pairs of homolgous chromosomes is four • only two of the four combination of daughter cells would result from meiosis of a single diploid cell b/c a single parent cell would have one or the other possible chromosomal arrangement at metaphase I but not both • the number of possible combinations of maternal and paternal chromsomes in the resulting gametes is 2^23 or about 8.4 million.
tRNA molecules trasnured from DNA templates (eukaryotic cell production of tRNA and function of tRNA in both eukaryotic and bacterial cells)
o eukaryotic cell: tRNA is made in the nucleus and then travelsfrom the nucleus to the cytoplasm o in both bacterial and eukaryotic cells each tRNa molecule is sued repeatedly-picking up its designated amino acid in the cytiosol, depositing this cargo into a polypeptide chain at the ribosome and then leaving the ribosome-ready to picik up another of the same amino acid
examples of point mutaitons
o ex: in individuals who are homozygous for the mutant allele the sickling of red blood cells caused by the altered hemoglobin produces the multiple symptoms associated with sickle-cell disease o ex: a heart condition called familial cardiomyopathy that is responsible from some incidents of sudden death in young athletes • point mutations in several genes that encode muscle proteins
food availability hypothesis
o hypothesis: anadromy will be more likely to evolve when ocean productivity is greater than that in neighboring freshwater and catadromy will evolve when freshwater food productivity exceeds that of ocean o sharp peak in freshwater productivity relative to marine waters in tropical latitude o marine waters significantly exceeds that of freshwater in temperate and polar latitude o certain fishes in temperate latitude have greater foraging opps. in oceans than in freshwater and others in tropical latitudes have greater foraging opps. in freshwater habitats o migration to freshwater (catadromy) more frequent in tropical latitude and migration to oceans (anadromy) is more frewuence in temperate latitude o where ocean more productive: diadromous fishes should be anadromous; where freshwater more productive :diadromous fish should be catadromous
error of neurolation
o in humans: an error in nueral tube formation results in spina bifida o spina bifida: a portion of the nueral tube fails to develop or close propely leabing an opening in the spinal colum an casing nerve damage
sister chromatids stay together due to sister chromatid cohesions (mitosis vs. meiosis)
o in mitosis: this attachment lasts until the end of metaphase when an enzyme cleave the cohesion freeing the sister chromatids to move to opposite poles of the cell o in meiosis: sister chromatid cohesion is released in two steps: one at the start of anaphase I and one at anaphase II;
three mechanisms contribute to the genetic variation arising from sexual reproduction
o independent assortment of chromosomes o crossing over o random fertilization
the break up of the phases (time-wise)
o m pahse occupy less than an hour o s pahse occur 10-12 o g 2 phase takes 4-6 hours o g1 phase takes 5-6 hours with variations
revision to the one gene-one enzyme hypothesis
o not all proteins are enzymes • keratin-the structural protein of animal hair- and the hormone insulin are two examples of nonenzyme proteins
five main themes of study of life
o organization o information o energy and matter o intereactions o evolution
complicating factors of experiment
o productivity is imperfectly correlated w/food availabltiy for species feeding at higher levels of fod chain o analysis overlooks fact that diadromous species move north or south after cross the ocean-freshwater broundary o selection for migration also affected by: • presence of competitor (food abundance) • predators and disease (survival)
the 5' cap and poly-A tail
o seem to facilitate the export of the mature mRNA from the nucleus o they help protect the mRNA from degradation by hydrolic enzymes o they help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm
• How did the interference evolve?
o some viruses have double-stranded RNA genomes o given that the cellular RNAi pathways can produce double stranded RNAs into homing devices that leas to destruction of related RNAs some scientists think that this pathways may have evolved as natural defense against infection by such viruses o the fact that RNAi can also affect the expression of nonviral cellular genes mat reflect a different evolutionary origin for the RNAi pathway o many species produce their own long, double-stranded RNA precursors to small RNAs such as siRNAs→once produced these RNAs can interfere with gene expression at stages other than translation
bacterial ribosome (structure)
o the structure clearly reflects its function of bringing mRNA together with tRNAs carrying amino acids o in addition to a binding site for mRNA each ribosome has three binding sites for tRNA • the P site • the E site • A site o The ribosome holds the tRNA and mRNA in close proximity and positions the new amino acid so that it can be added to the carboxyl end of the growing polypeptide→then catalyzed the formation of the peptide bond o As polypeptide becomes longer it passes through an exit tunnel in the ribosomes large subunit
cytokinesis in plant cells (which have walls) (telophase-->golgic apparatus vesicles--> cell plate-->cell wall)
o there is no cleavage furrow o during telophase vesciles derived from the golgi apparatus move along microtubules to the middle of the cell where they coalesce prudcing a cell plate o cell wall materials carried in vesicles collect inside the cell plate as it growns→cell plsate enlateges until surround memabres fusus w/the plasma memebrace along perimtiers of the cell→two daughter cells w/ own plasma maberace o a new cell wall arising from the contents of the cell plate fored btween the daughter cells
post-translational modification
o these may be required before the protein can begin doing its particular job in the cell o certain amino acid may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions o enzymes may remove one or more amino acids from the leading end of the polypeptide chain o a polypeptide chain may be enzymatically cleaved into two or more peices • ex: the protein insulin is first synthesized as a single polypeptide chain but becomes active only after an enzyme cuts out a central part of the chain→ a protein made up of two polypeptide chains connected by disulfide bridges
one type of damage : the covalent linking of thymine bases that are adjacent on a DNA strand
o thymine dimers causes the DNA to buckle and interfere with DNa replication o →can cause a disorder called xeroderma pigmentosum which in most cases is caused by an inherited defect in a nucleotide excision repair enzyme
neural plate-->neural tube-->brain
o →the nrual tube will becme the brian in the head and the spinal cord along the rest of the body o in contrast the notochord disspaears before brith although parts [ersist as the innr poritions of the disk
obligate vs facultative migration
obligate=individuals must migrate facultive=individuals chose to migrate
interphase (G1, S and G2 Phases)
often accounts for about 90% of the cycle. Interphase can be divided into subpahses G1 phase, S phase (synthesis) and G2 phase. o G pahses misnamed as gaps b/c the cells appeared inative o G pahses allow intense metabolic activity and growth occur hroughout inteprahse o during all three subphases of interaphse a cell grows by produing proteins and cytoplasmic organelles such as itochondria and endoplasmic reticulum o duplication of the chromsomes occur entirely during the S phase
actin filament and myosin
on the cytoplasmic side of he furrow is a contractile ring of actin microfilament assoiacted with molecules of the protein myosin o the actin microfilaments interact w. the myosin molecules causing the ring to contact
cytoplasmic side of furrow and actin microfilaments
on the cytoplasmic side of he furrow is a contractile ring of actin microfilament assoiacted with molecules of the protein myosin o the actin microfilaments interact w. the myosin molecules causing the ring to contact
differentiation
once it has undergone determination an embryonic cell can be experimentally placed in another location in the embryo and it will still differentiation into the cell type that is its normal fate ="the process by which a cell attaints its determinted fate"
Controlled experiment
one that is degined to compare an experimental group with a control group; groups designed t only differ in one factor
Darwins Conclusion
over many generations a higher and higher propoton of indivduals in a pop will have the advanteagous traits
Testing of chemical mutations
preliminary screening of chemicals to identify those that may cause cancers • makes sense because most carcinogens are mutagenic
inductive reasoning
process of deriving generalization from a large number of specific overvations
Binary Fission in Bacteria
prokaryoties can under a type of repodurction in which the cell grows to roughly double its size and then divides to form two cells
mitosis stages
prophase, prometaphase, metaphase, anaphase and telophase
cohesis
protein complexes that sister chromatids attach to
motor proteins in the kinetochores
proteins that "walk" the chromosomes along the microtubules which depolymerize at their kinetochore
Cadherins
proteins that help bind cells together, mediated by Ca++ ions.
Initiation of Translation and mRNA Degradation
ranslation presents another opportunity for regulating gene expression: such regulation occurs most commonly at the initiation stage
• Reading frame
reading the genetic symbols in the correct groupings" o Important in the molecular language of cells o →although a genetic message is written with no spaces between the codons the cells protein synthesizing machinery reads the message as a series of non-overlapping three-letter words
data
recordd overvations o data can be qualitative or quantitative o usually reached by the use of statistics in order to determine whether or not reults significant or not
gametes
reproductive cells o have one set or half as many chromosomes as somatic cells
differentiation
resulting specialization in structure and function(of cells)
Ribosomes (general function)
ribosomes facilitate the specific coupling of tRNA anticodon with mRNA cods during protein synthesis
Concept 1.3: In tudiying nature, scientists make observations and form and test hypotheses:
scineitsts use a process of inqury that includes making observatons, forming a logicacal, testable explenations (hypotheses) and ttesting them in testing a hypothesis more obserbations may inspire revision of the original hypothesis or formation of a new one, thus leading fto futher testing
Control elements
segments of noncoding DNA that serve as binding sites for the proteinss called transcription factors
induction
singals causing changes in the target cells
microRNAs
small single-stranded RNA molecules capable of binding to complementary sequences in mRNA molecules"
anadromous
species that migrate from freshwater and feed in the ocean
catadromous
species that migrate from the ocean and feed in freshwater
o A DNA binding domain
structure that bind to DNA
DNA
sturcutres called chrmosones contain genetic material in the form of DNA o Each time a cell divides, the DNA is first replicated, or copied, and each of the two ceullular offspring inherits a complete set of chromosoems (identical to that of parents) o Each chromosome contains one ver long DNA molecules with hundred or theounsds of genes, each a section of the DNA pf the chromosoms
Independent variable
that which is inherent and is the factor different between groups
Synapsis
the DNA breaks are closed up so that each broken end is joined to the corresponding segment of the non-sister chromatid→a paternal chromatid is joined to a piece of maternal chromatid o These points of crossing over become visible as chisma the synaptonemal complex disassembles and the homologs move slightly apart from each other • The homologs remain attached because sister chromatids are still held together by sister chromatid cohesion even though some of the DNA may no longer be attached to its original chromosomes • At least one crossover per chromosome must occur in order for the homologous pair to stay together as it moves to the metaphase I plate
osmoregulation
the active regulation of the osmotic pressure of an organism's fluids to maintain the homeostasis of the organism's water content; that is, it keeps the organism's fluids from becoming too diluted or too concentrated,"
communities
the array of organisms inhabiting a particular exosystem
Origins of Genetic Variation Among Offspring
the behavior of chromosomes during meiosis and fertilization is responsible for most of the variation that arises in each generation
• RNA interference
the blocking of gene expression by siRNAs"
taxonomy
the branch of biology that names and classifies pecies, formalizes this rdering os species into groups of increasing breadth, based on the degree to which they share characteristics
morphogenesis
the cellular and tissue based processes by which the animal body takes shape
Building a Structural Model of DNA: Scientific Inquiry
the challenge was to determine how the structure of DNA could account for its role in inheritance
four extramembryonic membranes
the chorion, allantois, amnion and yolk sac in all thse grups such mebrances provide a life support sustem for further embryonic development
cleavage furrow-->production of two cells
the cleavage furrow deepns until the parent cell is punched in two producing two completedly sperated cells each w/ its iwn nucleus and own share of cystosol, organlelles and other subcellular sturcutures
chromatin
the complex of protein and DNA within a cell" in the cell: eukaryotic DNA is precisely combined with a large amount of protein together this complex of DNA and protein called chromatin fits into the nucleus through an elaborate, multilevel system of packing
cytokinesis
the division of the cytoplasm
mitosis
the division of the genetic material in the nucleus, is usually followed immediately by cytokinesis o one cell has become two, each the genetic equivalent of the parent cell
chromatin
the entire complex of DNA and preoteins that is the building material of the chomosom o varies in its dgree of condensation during cell divison
Genome
the entire lbrary of genrtic insturctions that an organism inherits
gene expression
the entire process by which the finromation in a gene directs the manufactoru of a cellular product
Proteome
the entire set of proteins expressed by a given cell or group of cells
meiosis II
the equational division sister chromatids separates→producing haploid daughter cells
Transcription initiation complex
the eukaryotic gene and the DNA elements that control is; assembles on the promoter sequence ad the "upstream" end of the gene" o RNA polymerase II then proceeds to transcribe the gene synthesizing a primary RNA transcript (pre-mRNA) RNA processing includes enzymatin addition of a 5'cap and a poly-A tail as well as splicing out of introns to yield a mature mRNA o Associated with most eukaryotic genes are multiple control elements →regulate transcription →critical to the precise regulation of gene expression seen in different cell types
zona pellucida
the extraceullular matric of the egg
wobble
the flexible base paring at this codon position-third position"
Fertilization:
the formaitn of a diploid zygote from a halpid edd ad sperm
organogenesis
the formation of organs
"family tree" (Darwin's 14 Finches)
the fourteen finches that Darwin initially discovered and study on the Galapagos o eacg specieis is ne tig of a ranching tree of life extending backin time through ancestral species more and more remote; those very siiliar share a common ancestor at a relatively recent brach pont on the tree of life
observation
the gathering of information either through direct use of the senses or with the hekp of tools such as microscope, thermoemters and balances that extend our sences
during transcription
the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized o for each gene only one of the two DNA strands is transcribed
Independent Assortment of Chromosomes: Metaphase I
the homolgous pairs, each consist of one maternal and one paternal chromosome, are situated at the metaphase plate o Each pair may orient with either its maternal or paternal homolog closer to a given pole-its orientation is as random as flipping a coin; 50% chance that a particular daughter cell of meiosis will get the maternal chromosome of a certain homolgous pair and a 50% chance that it will get the paternal chromosome o b/c each pair of homologous chromosomes is positioned indepdnentely of the other pairs at metaphase I the first meiotic division results in each pair sorting its maternal and paternal homologs into daughter cells independently of every other pair
structure and function ex (hummingbirds)
the hummingbirds anatamon allows the wings to rotate at the shoulder, so hummbingbrds have ability to fly backward or stay in place
length of time of functional protien and selective degradation
the length of time each protein functions in the cell is strictly regulated by means of selective degradation o many proteins such a cycline must be relatively short-lived if the cell is to function appropriately o to mark a particular protein for destruction the cell commonly attaches molecules of a small protein called ubiquitin to the protein→giant proteins complexes called proteasomes then recognize the uniquitn tagged proteins and degrade them
cell cycle
the lufe of a cell from the time it is frist formed during dicion sof a prent cell until its own division into two daughter cells"
metaphase plate
the name for the plate where the centromeres end up during metaphase; not a physical cellular structur
anticodon
the particular nucleotide triplet that base pairs to a specific mRNA codon"
Elongation
the polymerase goes downstream, unwinding the DNA and elongating the RNA transcript 5'→3'-→the DNA strands re-form a double helix
arm
the portion of a chromatid to either side of the centromere
gene expression
the process by which DNA directs the synthesis of proteins • the expression of genes that code for proteins stages: o transcription & translation
determination
the process by which a group of cells become commited to a particular fate
Differentiation:
the process by which cells become specialized in structure and function
Genomics
the process by which researchers study whole sets of genes in one or more speciies
alternative RNA splicing
the process in which a a single gene can encode more than one kind of polypeptide" o ex: differences in fruit flies are largely due to difference in how males and females splice the RNA transcribed from certain genes o one reason humans can get alone with about the same number of genes as a nematode o the number of different protein products an organisms produces can be much greater than its number of genes
Pattern formation
the process in which cytoplasmic determinants and inductive signals both contiruted to the development of a spatial rognaization in which the tissues and organs of an orgnasm aaall in their characteristic places
meiosis
the process in which gametes (eggs and sperm) are produced which yields daughter cells with only one set of chromosomes o occurs only in the overies or testes (the gonads) o generating gametes meisosi reduces the chromosome number from two sets to one (23 chromosomes) but fertilization fses two gamets together and returns the chromosome number to 46 (two sets)
diadromous migration
the process in which some fish species migrate form freshwater and feed in the ocean (adronomous) and others migrate from the ocean and feed in freshwater (catadromous
sister chromatid cohesion
the process in which the sister chromatids attach to the cohesins the two chromatids (each contaiting an identical DNA molecule) are initially attached all along their lengths by protein complexed called cohesins; this attachment is known as sister chromatid cohesion each sister chromatid has a centromere
evolution
the process of change that has transformed life on earth from its beginning to organisms of today
reductionism
the process of reduzing complex systems to simpler components that are more manageable to study →provides a neccesarly incomplete view of life on Earth
transformation
the process that causes cells to behave like cancerl cells (cells in culut that aquir the abluty to divide indefinitely)
feedback regulation
the putput or pdouct of a process regulated that very pcoess
meiosis I
the reducing division b/c it reduces the number of chromosome set from two to one
at the onset of anaphase I
the release of cohesion along sister chromatid arms allow homologs to separate
anaphase II
the release of sister chromatid cohesion at the centromeres allow the sister chromatids to seperate
cell division
the reproduction of cells
polyribosomes
the result of a number of ribosomes trailing along the mRNA molecule" o enable a cell to make many copies of a polypeptide very quickly
biology
the scientific study of life
bacteria initiation
the small subunit can bind these two in either order: it binds the mRNA at a specific RNA sequence just upstream to the stat codon , AUG
Metastasis
the spread of cancels cells to locations distance from their orginal site
template strand
the strand of DNA being transcribed that provides the template for the sequence of nucleotides in an RNA transcript"
Transcription unit
the stretch of DNA downstream from the promoter that is transcribed into an RNA molecule"
Proteomics
the sudy of sets of protetins and their propeoeties
Conservative model
the two parental strands somehow come back together after the process; the parental molecule is conserved"
genes
the units of inheritance; they encode the information necessary to buld allof te mlvules synthesized with a cell, which in turn eastablush that cells indentity and function
Bioinformatics
the use of computational tools to sotre, organize, and analze the huge volume of data
organelles
the varios functional components present in a cell
tissue-specific proteins
these prteins are found only a sepcfic cell type and give the cell tis characteristic structure and function • the first evidiedence of differentitation is the appearance of mRNAs for these proteins • on the molecular elvel different sets of genes are sequeantially expressed ina regulated manner as new cells arise from division of their recurosors