Bio Exam #4 PDF

Exam #4 Chapter 14: Gene Expression: From Gene to Protein Intro: ○ Gene Expression: process by which DNA directs the synthesis of proteins ○ Proteins: link between genotype and phenotype ○ With the enzyme in the protein not working, the pigment doesn’t show up 14...

Exam #4 Chapter 14: Gene Expression: From Gene to Protein Intro: ○ Gene Expression: process by which DNA directs the synthesis of proteins ○ Proteins: link between genotype and phenotype ○ With the enzyme in the protein not working, the pigment doesn’t show up 14.1: Genes Specify Proteins via Transcription and Translation ○ Inherited traits are determined by genes with information content in the form of nucleotide sequence DNA leads traits by directing the synthesis of proteins and RNA molecules in protein synthesis (Gene Expression) Ex. coat and skin color ○ Gene Expression Two Processes where the expression of genes code for proteins: Transcription and Translation ○ Evidence from the Study of Metabolic Defects In 1902, a physician, Archibald Garrod, suggested that genes dictate phenotypes (particularly in humans) through enzymes that catalyze specific reactions Ex. alkaptonuria: black urine with the chemical alkapton ○ Results because of a missing enzyme/genetically inherited He thought that symptoms of a inherited disease reflect an inability to make a certain enzyme Cells synthesize and degrade molecules in a series of steps → metabolic pathway ○ If one step is missing, one enzyme will be more present than another ○ Ex. synthesis of the pigments give a donkey its fur color ○ Nutritional Mutants: Scientific Inquiry Beadle and Tatum began studying haploid bread mold because it was easier to detect recessive mutations (unlike the diploid organisms that Morgan studied) They studied mutations that altered the ability of the fungus to grow on minimal medium ○ Minimal medium: contain minimal nutrients upon which wild-type bread mold can grow They generated nutritional mutants, each of which was unable to synthesize a particular essential nutrient Advantages of the Neurospora species  Easy to grow Modest food requirements Approach of Beadle and Tatum 1) Cells placed on a complete medium 2) Cells are subjected to X-rays (help to generate mutations/break the chromosome) 3) Surviving cells form a colonies 4) Cells placed in minimal medium (glucose and some salts). Nutritional mutants are identified 5) Nutritional mutants placed in vials with a variety of media Conclusion: The researchers amassed a valuable collection of mutant strains Ex. one set of mutants all required arginine for growth It was determined that different classes of these mutants were blocked at a different step in the biochemical pathway for arginine biosynthesis One Gene-One Enzyme Hypothesis The function of a gene is to dictate the production of a specific enzyme A mutation in a gene causes a faulty enzyme that leads to an identifiable conditions ○ Ex. albino donkeys lack tyrosinase (a dark pigment) ○ The Products of Gene Expression: A Developing Story Some proteins (keratin, insulin) are not enzymes (one gene-one protein) Many proteins have several polypeptides (hemoglobin)→ (each has its own gene) → restated as the one gene-one polypeptide hypothesis ○ Basic Principles of Transcription and Translation Terms RNA ○ Chemically similar to DNA but RNA has a ribose sugar instead of deoxyribose ○ Base is Uracil instead of Thymine ○ Single-stranded ○ Getting from DNA to protein requires: transcription and translation Transcription: synthesis of RNA using information in DNA ○ Produces messenger RNA (mRNA) Translation: synthesis of a polypeptide, using information in the mRNA  ○ Ribosomes: sites of translation Pathway (DNA → RNA → Protein) Bacterial Cell ○ In bacteria, translation of mRNA can begin before transcription finishes ○ Both processes are in the cytoplasm Eukaryotic Cell ○ In eukaryotes: nuclear envelope separates transcription from translation mRNA must be transported out of the nucleus to be translated ○ Translation is in the cytoplasm ○ RNA transcripts are modified through RNA processing → mRNA Terms Primary transcript: initial RNA transcript from any gene prior to processing Central Dogma: concept that cells are governed by a cellular chain ○ The Genetic Code There are 4 nucleotide bases to specify 20 amino acids (so a single nucleotide does not correspond to ONE amino acid) ○ Codons: Triplets of Nucleotides Terms Triplet code: series of nonoverlapping, three-nucleotide words Template Strand: provides a template for an RNA transcript (read 3’ to 5’) Codons: mRNA base triplets (read in the 5’ to 3’) Process 1) the words of a genes are transcribed into complementary nonoverlapping three-nucleotide words of mRNA 2) these words are translated into a chain of amino acids → polypeptide 3) the template strand is always the same strand for any given gene (opposite strand may function as the template for a different gene) 4) RNA that is synthesized is complementary to template strand ○ Antiparallel 5) codons are read during translation ○ Each codon specifies the amino acid to be placed along the polypeptide  6) the nontemplate strand is also called the coding strand because it has the same amino acid information as the RNA molecule ○ Cracking the Code All 64 codons were deciphered by mid-1960s 61 → amino acids 3 → “stop” signals to end translation (UAA, UAG, UGA) Genetic Code is redundant: more than one codon may specify a particular amino acid No codon specifies more than one amino acid Codons must be read in the correct reading frame (correct groupings) for the polypeptide to be produced Read one at a time in a non overlapping fashion ○ Evolution of the Genetic Code Genetic code is nearly universal Genes can be transcribed and translation after being transplanted from one species to another Operates in the common ancestor of all present-day organisms 14.2: Transcription is the DNA-directed Synthesis of RNA ○ Transcription is the FIRST stage of gene expression ○ Molecular Components of Transcription Steps RNA polymerases ○ RNA polymerase pries DNA strands apart and joins the complementary RNA nucleotides ○ RNA polymerases ONLY assembles polypeptides in the 5’ to 3’ ○ RNA polymerases can start a chain without a primer (unlike DNA polymerases) The DNA sequence where RNA polymerases attaches is called the promoter ○ In bacteria the sequence signaling the end of transcription is the terminator Transcription Unit: stretch of DNA that is transcribed Bacteria have one RNA polymerase: eukaryotes have at least three types ○ Eukaryotes: pre-mRNA is synthesized by RNA polymerase II ○ Steps of Transcription: Initiation, Elongation and Termination RNA Polymerase Binding and Initiation of Transcription  Promoter of a gene includes the start point and usually extends several dozen nucleotide pairs from start point (upstream) Transcription factors: mediate the binding of RNA polymerase and transcription initiation Transcription Initiation Complex: assembly of transcription factors and RNA polymerase II bound to a promoter TATA box: promoter DNA sequence (forms initiation complex in EUKARYOTES) Elongation of the RNA Strand RNA polymerase untwists the DNA, 10-20 bases at a time ○ Transcription occurs at a rate of 40 nucleotides per second (eukaryotes) A gene can be transcribed simultaneously by molecules of RNA polymerase (helping cells produce a lot of the protein) Termination of Transcription Bacteria ○ Polymerase stops transcription at the END of the terminator ○ mRNA is translated without modification Eukaryotes ○ RNA polymerase II transcribes polyadenylation signal sequence ○ RNA transcript is release 10-35 nucleotides past the sequence 14.3: Eukaryotic Cells Modify RNA after Transcription ○ Intro Enzymes modify pre-mRNA before genetic signals are given to the cytoplasm During RNA processing Both ends of primary transcript are altered Some interior parts are cut out and others are spliced together ○ Alternation of mRNA Ends Each end is modified in a certain way 5’ end: gets a modified G nucleotide 5’ cap 3’ end: poly-A tail Modification share functions Export of mRNA to cytoplasm Protects mRNA from hydrolytic enzymes Helps ribosomes attach to the 5’ end ○ Split Genes and RNA Splicing  RNA splicing: portions of the RNA molecule are removed and remaining portions reconnect (carried out by spliceosomes) Introns: noncoding regions Exons: other regions translated into amino acid sequences Introns are cut out and exons are joined together Alternative RNA splicing: many genes give rise to two or more different polypeptides Spliceosomes: consist of proteins and small RNA Small RNA: catalyze splicing process ○ Ribozymes RNA molecules that function as enzymes RNA splicing can occur without proteins or other RNA molecules Introns can catalyze their own splicing Discovery of ribozymes invalidated the idea that all biological catalysts are proteins 14.4: Translation ○ Genetic information flows from mRNA to protein through translation ○ Molecular Components of Translation Transfer RNA: helps a cell translate an mRNA message into protein Transfer amino acids to growing polypeptide in a ribosome ○ Structure and Function of Transfer RNA Enables translation of a mRNA codon into a specific amino acid Structure tRNA contains an amino acid at one end and nucleotide triplet (that can base-pair with complementary codon) on the other tRNA consists of a single RNA strand → about 80 nucleotides long tRNA molecules can base-pair with themselves ○ Flattened, it looks like a cloverleaf Roughly L-shaped; one end contains the anticodon that base-pairs with mRNA codon Two Types of Molecular Recognition Aminoacyl-t RNA synthetase: conducts correct matching between a tRNA and an amino acid (present in eukaryotes and bacteria) Complementary pairing between tRNA anticodon and mRNA codon Wobble: flexible pairing at the third base of a codon Allows some tRNA to bind to more than one codon ○ Structure and Function of Ribosomes  Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons Large and small ribosomal are made of proteins and ribosomal RNA Join to form a complete ribosome only when attached to an mRNA Three Binding Sites for tRNA P site: holds tRNA that carries the growing chain A site: holds tRNA that carries the next amino acids E site: exit site, where discharged tRNA leaves ○ Building a Polypeptide Three Stages of Translation Require protein “factors” aiding in the translation process Energy is provided by GTP ○ Ribosome Association and Initiation of Translation 1) Initiation stage of translation bring together mRNA and the two ribosomal subunits 2) A small ribosomal subunit binds with mRNA and a initiator tRNA 3) The small subunit moves along the mRNA until it reaches the start codon Important because it establishes the reading frame for mRNA 4) addition of the large ribosomal subunit completes formation of translation initiation complex Chapter 15: Regulation of Gene Expression 15.1: Bacteria Often Respond to Environmental Change by Regulating Transcription ○ Natural selection has favored bacteria that produce only the gene products needed by cell ○ A cell can regulate the production of enzymes by feedback inhibition / gene regulation Controlled by operon model ○ Operons: The Basic Concept Operon: a single promoter serving a set of functionally related genes Controlled by a single “on-off switch” (a segment of DNA called an operator, usually positioned within the promoter) The entire stretch of DNA including the operator, promoter, and the genes they control The operon can be switched off by a protein: repressor Binds to operator and blocks the attachment of RNA polymerase Product of a separate regulatory gene, which is not part of the operon  Can be in an active or inactive form, depending on the presence of other molecules Corepressor: a molecule that cooperates with a repressor protein to switch an operon off Ex. tryptophan operon is a repressible operon (on by default and the genes for tryptophan synthesis are transcribed) An operator alternates between two states: one with repressor bound and one without Tryptophan When tryptophan is present, it binds to the trp repressor protein, which then turns operon off Repressor is active only in the presence of tryptophan, the trp operon is turned off if tryptophan levels are high ○ Repressible and Inducible Operons: Two Types of Negative Gene Regulation Repressible: one that is usually on; binding of a repressor to the operator shuts off transcription Ex. trp operon is repressible operon Inducible: one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription Ex. lac operon → contains genes that code for enzymes that function in the use of the sugar, lactose ○ By itself, it is active and switches the lac operon off by binding the operator An inducer (allolactose) inactivates the repressor to turn the lac operon on Enzymes of the lactose pathway are called inducible enzymes Enzymes for tryptophan synthesis are called repressible enzymes Repressible enzymes usually function in anabolic pathways; repressed by high levels of the end product Inducible enzymes usually function in catabolic pathways; synthesis induced by a chemical signal Regulation of trp and lac operons involves negative control of genes because operons are switched off by active form of repressor ○ Positive Gene Regulation E. coli preferably uses glucose when it is present If glucose is limited, CRP (cAMP receptor protein) acts as an activator of transcription ○ Activated by binding with cyclic AMP (cAMP)  ○ The activated CRP attaches to the promoter of the lac operon → increasing affinity of RNA/accelerates transcription If there is an increase in glucose ○ cAMP levels fall ○ CRP detaches from lac operon ○ Transcription proceeds at a low rate CRP helps regulate other operons that encode enzymes in catabolic pathways → affecting expression of more than 100 genes in E.coli 15.2: Eukaryotic Gene Expression is Regulated at Many Stages ○ Organisms must regulate which genes are expressed at any time ○ Different Gene Expression Almost all cells in an organism contain an identical organism Differences between cell types result from differential gene expression Expression of different genes by cells with the same genome Abnormalities in gene expression → serious imbalances and diseases ○ Regulation of Chromatin Structure Structural organization of chromatin packs DNA into a compact from and helps to regulate gene expression The location of a gene promoter relative to nucleosomes and scaffold attachment sites can influence gene transcription Genes within highly condensed heterochromatin are not usually expressed Modification to histone proteins and DNA can influence chromatin structure and gene expression ○ Histone Modification and DNA Methylation Histone Acetylation: acetyl groups are attached to amino acids in histone tails Loosens chromatin structure → promotes initiation of transcription Addition of methyl groups can condense chromatin and lead to reduced transcription Addition of a chemical group can create a new binding site for enzymes DNA methylation: addition of methyl groups to certain bases in DNA, usually cytosine Individual genes are more heavily methylated where there are not expressed Once methylated genes usually remain through cell divisions After replication, enzymes methylate the daughter strand ○ Epigenetic Inheritance  Chromatin modifications may not alter DNA but they can be passed to future generations Epigenetic Inheritance: Inheritance of traits not directly involving the nucleotide sequence Epigenetic modification can be reversed (unlike mutations in DNA sequence) ○ Regulation of Transcription Initation Chromatin-modifying enzymes provide initial control of gene expression Allows it by making a region of DNA less or more able to bind the transcription machinery ○ Organization of a Typical Eukaryotic Gene and Its Transcript Control elements: associated with most eukaryotic genes Segments of noncoding DNA serve as binding site for transcription factors Critical for precise regulation of gene expression in different cell types ○ The Roles of General and Specific Transcription Factors General transcription factors act at the promoto Some genes require specific factors that binds to control elements close to or far from the promoter ○ General Transcription Factors at the Promoter Initiating Transcription Eukaryotic RNA polymerase requires assistance of transcription factors A few of these factors bind to a DNA sequence but most bind to proteins Interaction of general transcription factors and RNA polymerase II with a promoter → low rate of initiation ○ Enhancers and Specific Transcription Factors Proximal control elements: located close to promoter Distal control elements (some called enhancers): far away from a gene or even in an intron A gene may have multiple nhancers, active at different times, cell types, or locations Activator: protein that binds to an enhancer and stimulates transcription of a gene Two domain: one that binds DNA, a second that activates transcription Bound activators: facilitate a sequence of protein-protein interactions resulting in the transcription of a given gene  Brought in contact with mediator protein through DNA bending The mediator proteins interact with proteins at the promoter The protein-protein interactions help to assemble and position the initiation complex on the promoter Some transcription factors function as repressors, inhibiting expression of a particular gene some repressors bind directly to control element DNA to block activator bindings Some interfere with the activator itself Some activators and repressors act indirectly by influencing chromatin structure to promote or stop transcription ○ Combinatorial Control of Gene Activation Eukaryotes Control of transcription depends on binding of activators to DNA Combination of control elements is important for transcription ○ Coordinately Controlled Genes in Eukaryotes Eukaryotic genes that are co-expressed are not organized into operons Can be scattered over different chromosomes but each has the same combination of the control elements Activator proteins → recognize specific control elements and promote transcription of genes Genes with same sets of control elements are activated by same chemical signals ○ Mechanisms of Post-Transcriptional Regulation Regulatory mechanisms operate at various stages after transcription Help to cell to rapidly go under gene expression ○ RNA Processing Alternative RNA Splicing: different mRNA molecules are produced from the same transcript, depending on what is treated as exons and introns Significantly expands the repertoire of a genome ○ Initiation of Translation and mRNA Degradation Initiation of translation can be blocked by regulatory proteins that bind to sequences or structures of mRNA Alternatively, translation may be regulated simultaneously Ex. translation initiation factors are simultaneously activated in an egg following fertilization Eukaryotic mRNA survives longer than prokaryotic mRNA Sequences that influence life span are in the untranslated region at the 3’ end ○ Protein Processing and Degradation  After translation, types of protein processing (cleavage and chemical modification) are subject to control The length of time a protein function is regulated by selective degradation To mark a protein for destruction, the cell attaches molecules of ubiquitin to the protein 15.3: Noncoding RNAs Play Multiple Roles in Controlling Gene Expression ○ Intro Protein-coding DNA is only 1.5% of the human genome A small fraction of non-protein-coding DNA consists of genes for RNAs (ribosomal and transfer RNA) A significant amount of genome is transcribed into noncoding RNAs (ncRNAs) ○ Effects on mRNAs by MicroRNAs and Interfering RNAs MicroRNAs (miRNAs): (20-25 nucleotides long): small, single-stranded RNA molecules that bind to complementary mRNA sequences Leads to degradation of mRNA/block translation multiplemRNAs Atleast ½ of the human genome are regulated by microRNAs Small interfering RNAs (siRNAs): same as RNA but form subtly different RNA precursors Inhibit expression of a single mRNA RNA interference (RNAi): inhibition of gene expression by siRNAs Used to disable specific genes to find out their function ○ Chromatin Remodeling and Effect on Transcription by Noncoding RNAs siRNAs are often required for the formation of heterochromatin at centromeres of chromosomes Interact with other noncoding ncRNAs and chromatin-modifying enzymes Leads to condensation of centromere chromatin → heterochromatin Piwi associated RNAs (pIRNAs): induce formation of heterochromatin Block expression of transposons (parasitic DNA elements in the genome) 15.4: Researchers can Monitor Expression of Specific Genes ○ Studying the Expression of Single Genes Nucleic acid hybridization: base pairing of a strand of a nucleic acid to its complementary sequence Nucleic acid probe: short, single-stranded DNA or RNA that is the complementary molecule  Each probe is labeled with a fluorescent tag to allow visualization in situ hybridization: allows us to see mRNA in lace in the intact organism Reverse transcriptase-polymerase chain reaction (RT-PCR): method for comparing amounts of specific mRNA in different samples Turns sample sets of mRNA into double-stranded DNA Relies on the activity of reverse transcriptase → complementary DNA Complementary DNA (cDNA): can synthesize a DNA copy of mRNA Once cDNA is produced, PCR is used to make many copies of the sequence of interest ○ Studying the Expression of Groups of Genes A DNA microarray contai ans tiny amounts of single-stranded DNA fragments This is called a DNA chip mRNA from cells of interested are isolated and converted into cDNAs cDNAs from two different samples are labeled with different tags Identify subsets of genes that are expressed differently in ONE sample Studies of genes expressed together in some tissues but not others can help for a understanding of diseases Ex. Testing gene expression in tumor cells compared to non tumor cells for identification of targets for therapy Chapter 16: Development, Stem Cells, and Cancer 16.1: A Program of Differential Gene Expression Leads to Different Cell Types in a Multicellular Organism ○ A fertilized egg gives rise to many cell types ○ Cells are highly predictive Organized into tissues, organs, systems and the organism ○ A Genetic Program for Embryonic Development Zygote → adult Results from cell division, differentiation and morphogenesis (mitotic processes) Cells increase in number but also become specialized in structure and function (mass increases) Cell differentiation: process by which cells become specialized in structure / function Morphogenesis: physical processes that give an organism its shape Differential Gene Expression: results from genes being regulated differently in each cell type  Sequential program of gene regulation that is carried out as cells divide ○ Cytoplasmic Determinants and Inductive Signals Cytoplasm: contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg Cytoplasmic Determinants: maternal substances in the egg that influence early development As zygote divides, resulting cells contain different cytoplasmic determinants → different gene expression Induction: signal molecules from embryonic cells cause transcriptional changes in nearby target cells Interactions induce differentiation of specialized cell types ○ Sequential Regulation of Gene Expression During Cellular Differentiation Determination: commits a cell irreversible to its final cell type Once a cell is determined, it can be placed in a different location in an embryo and still develop Precede differentiation ○ Differentiation of Cell Types The first evidence of differentiation is the production of mRNA for these proteins It is observed as changes in cellular structure To Study determination, researchers grew embryonic precursors cells They identified “master regulatory genes” whose protein products commit cells to muscle ○ Ex. myoD: transcription factor that targets genes encoding muscle-specific proteins ○ Apoptosis: A Type of Programmed Cell Death Apoptosis: “programmed cell death” Occurs in the mature organism in cells that are infected, damaged, or at the end of their functional lives Steps DNA is broken up and organelles / cytoplasmic components are fragmented Cells becomes multilobed and its contents are packaged in vesicles (“blebs”) The vesicles are engulfed by scavenger cells Apoptosis protects neighboring cells from damage by nearby dying cells Apoptosis is essential to development and maintenance Known to occur in multicellular fungi and single-celled yeasts  In vertebrates, apoptosis is essential for normal development or morphogenesis of hands or feet ○ Pattern Formation: Setting up the Body Plan Pattern formation: development of a spatial organization of tissues and organs IN ANIMALS, begins with establishment of major aces Ex. studied in fruit fly Positional information: molecular cues that control pattern formation, tells a cell its location relative to body axes Studying model organisms, understanding the genetics underlying development has progressed Easy to raise in lab and use in experiments ○ Life Cycle of Drosophila Fruit flies and other arthropods have a modular structure, composed of an ordered series of segments Cytoplasmic determinants in the unfertilized egg determine the anterior-posterior and dorsal-ventral body axes before fertilization The Drosophila eggs develop in the females’ ovary surrounded by ovarian cells called nurse and follicle cells After fertilization, embryonic development results in a segmented larva Larva forms a pupa within which it metamorphoses into an adult fly ○ Genetic Analysis of Early Development: Scientific Inquiry Edward B. Lewis, Christiane Volhard and Eric Wieschaus won a Nobel Prize for decoding pattern formation in Drosophila Studied mutations that led to extra wings or legs They found Homeotic genes: control pattern formation in late embryo, larva, and adult stages Embryonic lethals: mutations that cause death during embryonic or larval stages Identified 120 genes essential for normal segmentation patterns ○ Axis Establishment Maternal effect genes: encode cytoplasmic determinants that establish the axes of Drosophila When these genes are mutant in the mother, the phenotype is seen in the offspring Egg-polarity genes: control orientation of the egg and fly ○ Bicoid: A Morphogen That Determines Head Structures Bicoid: affects front half of the body  No bicoid → lacks front half of its body and has posterior structures at both ends Bicoid gene: required for setting up anterior end of the fly and might be concentration at the future anterior end of the embryo Highly concentrated at the anterior end Morphogens: establish an embryo’s axes and other features After the egg is fertilized, the mRNA is translated into Bicoid protein which diffuses from the anterior end Injection of the bicoid mRNA into various regions results in formation of anterior structures at site of injection Why was this research groundbreaking? Identified a specific protein required for steps in pattern formation Increased understanding of a mothers critical role in embryo development Demonstrated a gradient of morphogens that determine polarity and position in the embryo ○ Evolutionary Developmental Biology (“Evo-Devo”) A single mutation leads to a fly with legs emerging from its head Can these mutations contribute to evolution of novel body shapes? 16.2: Cloning Organisms Showed That Differentiated Cells Could Be “Reprogrammed” and Led to Production of Stem Cells ○ Intro In cloning, one or more organisms develop from a single cells without meiosis or fertilization Cloned individuals are genetically identical to the “parent” that donated the single cell Cloning arises from its potential to generate stem cells ○ Cloning Plants: Single-Cell Cultures F.C Steward and his students first cloned whole carrot plants in the 1950s Single differentiated cells incubated in culture medium were able to grow in adult plants Differentiation is not irreversible necessarily Totipotent: cells that give rise to all specialized cell types ○ Cloning Animals: Nuclear Transplantation The nucleus of an unfertilized egg cell or zygote is replaced w the nucleus of a differentiated cell Nuclear transplantation or somatic cells nuclear transfer Ex. frog embryos showed that transplanted nucleus can support normal development of an egg  The older the donor nucleus, lower percentage of normally developing tadpoles John Gurdon concluded that nuclear potential is restricted as development and differentiation proceed ○ Reproductive Cloning of Mammals 1997, Scottish researchers announced the birth of a lamb cloned from an adult sheep by nuclear transplantation Premature death led to the speculation that cells were not as healthy → incomplete reprogramming of original transplanted nucleus Cloned animals of the same species are not always identical CC (carbon copy) was the first cat cloned; differed from female “parent” ○ Epigenetic Differences in Cloned Animals Many cloned animals exhibit defects Epigenetic changes must be reversed in the nucleus from donor animal to be expressed or repressed appropriately ○ Stem Cells of Animals A stem cell is a relatively unspecialized cell It can both reproduce itself indefinitely and differentiate into specialized cells of one or more types ○ Embryonic and Adult Stem Cells Pluripotent: early animal embryos containing stem cells that can differentiate into any cell type Embryonic stem cells can reproduce indefinitely ○ Induced Pluripotent Stem Cells (iPS) Researchers can “deprogram” cells to act like ES cells using retroviruses The retroviruses: introduce more cloned copies of stem cells regulatory genes iPS cells can perform most functions of ES cells but there are difference in gene expression and cellular functions Potential Uses for iPS cells Patients suffering from diseases can be reprogrammed into iPS cells to replace nonfunctional cells Age related macular degeneration and sight disorders are frequent targets of stem-cell therapy Researchers have made iPS cells from skin or other cells and caused them to differentiate into retinal cells Implanted into retinas  16.3: Abnormal Regulation of Genes that Affect the Cell Cycle can Lead to Cancer ○ Gene regulation system that go wrong during cancer are the same systems that are involved in embryonic development, maintenance of stem cell populations and many others ○ Types of Genes Associated w Cancer Oncogenes: cancer-causing genes in certain viruses Proto-oncogenes (normal version of genes): code for proteins that stimulate normal cell growth and division Proto-oncogenes can be converted to oncogenes by Epigenetic changes that alter chromatin form and expression of proto-oncogenes Movement of the oncogene to a position near a promoter → increasing transcription Amplification → increasing number of copies of a proto-oncogene Point mutations in the proto-oncogene or its control elements → causing an increase in gene expression Tumor suppressor genes: encode proteins that hep prevent uncontrolled cell growth Repair damaged DNA Control cell adhesion Inhibit the cell cycle Mutations that decrease protein products of TS genes may contribute to cancer onset ○ Interference with Cell-Signaling Pathways Mutations in the ras proto-oncogene and p53 TS gene are common in human cancers Lead to production of a hyperactive Ras protein and increased cell division Activates a kinase cascade that lead to cell division Hyperactive versions of any members of the cascade → excessive cell division Mutations in the p53 gene prevent suppression of the cell cycle and excessive cell division In response, the normal p53 protein activate other proteins to stop cell cycle Also turns on genes directly involved in DNA repair ○ If it is not reparable, p53 activates “suicide” genes → apoptosis ○ The Multistep Model of Cancer Development Many mutations are needed for cancer (about half a dozen changes)  These changes generally include at least one active oncogene and loss of several TP genes (ras oncogene and mutated p53 gene are often involved) Incidence of cancer increases with age The multistep path is supported by studies of human colorectal cancer The first sign of colorectal cancer is a polyp, small benign growth in the colon lining ○ Inherited Predisposition and Factors Contributing to Cancer Individuals can inherit oncogenes or mutant allele of tumor suppressor genes Mutation: hereditary nonpolyposis colorectal cancer (HNPCC): autosomal dominant mutation that increases an individual’s risk of cancer ○ Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli (APC) is also common in individuals with colorectal cancer Mutations in BRCA1 or BRCA2 genes are found in at least 50% of inherited breast cancers Considered tumor-suppressor genes because their wild-type alleles protect against breast cancer and mutant alleles are recessive DNA breakage → cancer; risk of cancer can be lowered by minimizing DNA damage like ultraviolet radiation Viruses also play a role in about 15% of human cancer by donating an oncogene to a cell, disrupting a tumor-suppressor gene, or converting proto-oncogene → oncogene Chapter 18: Genomes and Their Evolution 18.1: Human Genome Project Fostered Development of Faster, Less Expensive Sequencing Techniques ○ Genomics Study of whole sets of genes and their interactions ○ Bioinformatics: application of computational methods to storage and analysis of biological data ○ Human Genome Project: began in 1990 and sequencing wass done by 2003 Original sequenced DNA was pooled from a few individuals Reference genome: full sequence representing genome of a species ○ Draft Human Pangenome Based on 47 individuals from various population Goal of mapping genome: determine complete nucleotide sequence Sequencing all 3 billion pairs in a haploid set presented a challenge  ○ MAJOR SUCCESS of the Human Genome Project: development of sequencing machines with automated technology for faster sequencing ○ Whole-genome shotgun approach Starts with cloning and sequencing random DNA fragments Powerful computer programs are used to assemble short overlapping sequence in a single sequence New Techniques Ex. Sequencing by Synthesis has resulted in massive increases in speed and decreases in the cost of sequencing genomes Allow direct sequencing of fragments without cloning Single long DNA strands up to 100,000 bases or more can be sequenced at one time ○ Metagenomics DNA from a group of species in environmental sample is collected and sequenced Computer software orts them and assembles into specific genomes The approach is applied to communities in environments that are diverse 18.2: Scientists Use Bioinformatics to Analyze Genomes and their Functions ○ HGP established databases and softwares to make data available on Internet ○ Centralized Resources for Analyzing Genome Sequences Examples NIH, NCBI European Molecular Biology Lab DNA Data Bank of Japan BGI in China Ex. Gen Baknk: NCBI database of sequences is constantly updated Ex. BLAST allows online visitors to search GenBank for A specific DNA sequence Predicted protein sequence Common stretches of amino acids in a protein and three-dimensional model of domain Sequences of DNA or proteins can be diagrammed as a evolutionary tree ○ Understanding the Functions of Protein-Coding Genes DNA sequence may vary more than protein sequence does Scientists interested in proteins compare predicted sequence with that of other proteins Protein function can be deduced from sequence similarity or a combination of biochemical and functional studies Involves knocking out the gene to see how the phenotype is affected  ○ Understanding Genes and Gene Expression at the Systems Level A project called ENCODE ran from 2003-2012 Aim was to learn about functionally important elements in the genome: protein-coding genes, genes for non-coding RNA, chromatin structure, sequences that regulate gene expression Analyzed cultured cells About 75% of the genome is transcribed in at least one of the cell types studied However, less than 2% codes for proteins THe Roadmap Epigenomics Project set out to characterize the epigenome of hundreds of human cell types ○ Systems Biology Proteomics: systematic study of full protein sets expressed by cells Systems biology: aims to model dynamic behavior of whole biological systems based on study of interactions among system’s parts ○ Application of Systems Biology to Medicine A systems biology approach has several medical application Ex. Cancer Genome Atlas Project: set out to determine how changes in biological systems lead to three types of cancer Silicon and glass “chips” have been produced that hold a microarray of most known human genes Microarrays allow analysis of which genes are over-or under expressed in cancers May allow physicians to tailor patients’ treatment to their unique genetic makeup Medical records may include an individual's DNA sequence These sequences can be used for personalized medicine 18.3: Genomes Vary in Size, Number of Genes, and Gene Density ○ Ten of thousands of genomes are in progress or considered permanent drafts Around 50,000 metagenomes are also in progress ○ Genome Size Genomes of most bacteria and archaea range from 1-6 million base pairs Genomes of eukaryotes tend to be larger Most plants and animals have genomes greater than at least 100 Mb; humans have 3,000 Mb ** With each domain, no systematic relationship between genome size and a phenotype ○ Number of Genes Free living bacteria have 1,500 - 7,500 genes Unicellular fungi have abt 5,000 genes  Multicellular eukaryotes can have up to 40,000 genes Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts ○ Gene Density and Noncoding DNA Human and other mammals have lowest gene density Multicellular eukaryotes have many introns within genes Also lots of noncoding DNA between genes 18.4: Multicellular Eukaryotes Have a Lot of Noncoding DNA and Many Multigene Families ○ Bulk of most eukaryotic genomes encodes neither proteins nor functional RNAs Sequencing of genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs (a quarter of genome codes for introns) ○ DNA between functional genes includes Unique noncoding sequences such as gene fragments Pseudogenes: former genes that have accumulated mutations and are nonfunctional Repetitive DNA: present in multiple copies of genome ○ Some noncoding sequences are identical in humans, rats, and mice ○ Transposable Elements and Related Sequences Transposable Elements: both prokaryotes and eukaryotes have stretches of DNA that can move from one location to another Movement: transposition About 75% of repetitive DNA is made up of transposable elements ○ Movement of Transposons and Retrotransposons Two Types Transposons ○ “Cut and paste” or “copy and paste” ○ Require an enzyme called transposase to move Retrotransposons ○ RNA intermediate and leaves a copy behind Intermediate must be converted back to DNA by reverse transcriptase ○ Sequence Related to Transposable Elements In human and other primates, a large portion of transposable element-related DNA consists of Alu elements Transcribed into RNA molecules About 17% of human genome is made up of sequence called LINE-1 Long (6,500 pairs) Low rate of transposition  Transposable elements may encode proteins therefore elements are noncoding DNA ○ Other Repetitive DNA, Including Simple Sequence DNA About 14% of genome consists of repetitive DNA About a ⅓ of this consists of duplication of long sequences of DNA In contrast, simple sequence DNA contains many copies of repeated short sequences Short tandem repeat: series of repeating units of two to five nucleotides Repeat number for STRs can vary among sites or individuals Can be used to identify a unique set of genetic markers for an individual: genetic profile Simple sequence DNA makes up 3% of genome Located on tips and centromeres in chromosomes ○ Genes and Multigene Families Multigene families: collections of identical or very similar genes Some Multigene families consists of identical DNA sequences such as those that code for rRNA products 18.5: Duplication, Rearrangement, and Mutation of DNA Contribute to Genome Evolution