Ch. 18 - 24 notes for exam #4
Ch. 18 - 24 notes for exam #4 LIFE 102-220
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This 29 page Class Notes was uploaded by Bailey Sniffin on Wednesday January 20, 2016. The Class Notes belongs to LIFE 102-220 at Colorado State University taught by Dr. Patricia Bedinger in Fall 2015. Since its upload, it has received 19 views. For similar materials see Attributes of Living Systems (Honors) in Biology at Colorado State University.
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Date Created: 01/20/16
CHAPTER 17 Transcription 1. Transcription factors bind to promoter (+ enhancers) 2. RNA polymerase binds to promoters 3. Synthesis of a transcript begins (RNA molecule) Translation 1. A charged tRNA binds to the A site 2. A peptide bond forms 3. mRNA shifts relative to the ribosome (translocation) 4. Uncharged tRNA is released Translation converts from one language to another o A nucleic acid sequence into an amino acid sequence 3 nucleotides together make one codon, these encode all 20 possible amino acids The genetic code is redundant but not ambiguous and is almost universal Translation requires mRNA, charged transfer RNAs, energy, and complex molecular machines called ribosomes There are 20 different amino acids and 4 different nucleotides So code cannot be 1:1 or 2:1 but 3:1 gives us 64 possible combinations of nucleotides o The code is based on nucleotide triplets = codons The Genetic Code It’s redundant: there is often more than one codon per amino acid o Ex. UUU = phe and UUC = phe Often it’s the 3 base that varies This example is shown in the upper left corner of the table above It’s NOT ambiguous: UUU always encodes phe and no other amino acid It’s (almost) universal: from bacteria to humans, this IS the genetic code Nonoverlapping reading Frame: from first AUG (encodes met) to the first stop, shift to the next 3 nucleotides Translation (Protein Synthesis) We need 3 things: o 1. An mRNA containing codons, including a start codon (AUG) and a stop codon (UAA UGA or UAG) o 2. We need a dictionary = “charged” tRNAs One end recognized a codon (the anticodon) one end has the right amino acid attached Enzymes called tRNA synthetases add the right amino acid to the right tRNA Sometimes called the “second genetic code” Make the covalent link between the amino acid and tRNA Requires energy in the form of ATP hydrolysis o 3. We need machines! Ribosomes – rRNA + proteins Ribosomes have two subunits, large and small, that come together 3 things we need for protein synthesis: o mRNA o Charged tRNAs o Ribosomes Initiation Formation of an initiation complex: o 1. mRNA o 2. Special initiator tRNA in the P site o 3. Ribosomal subunits Requires proteins called Initiation Factors and energy in the form of GTP hydrolysis Elongation (which itself has 3 parts): o 1. A charged tRNA enter the A (amino acid) site, the anticodon Hbonds with the codon of the mRNA o 2. Peptide bond is formed between aa at P (peptide) site and aa at A site (by RNA in ribosome = another ribozyme) o 3. Translocation: mRNA, with tRNA with attached polypeptide shifts to the P site, “naked” tRNA at P site moves to E, exit site and leaves Elongation requires proteins called Elongation Factors and energy in the form of GTP hydrolysis Termination When a stop codon is reached in the mRNA, there is no charged tRNA that recognizes it o A release factor binds, releases protein, and disrupts the complex On any single mRNA, there are usually many ribosomes translating it at one time = poly(ribo)somes Cellular Destinations of Proteins How do proteins get to their final destination in the cell? o In general, the first few amino acids (usually at the Nterminus) contain targeting information For example: o Entering the endomembrane system (RER, Golgi, lysosomes, Plasma membrane, secretion out of cell) Getting into the RER: o The first few amino acids are very specific and are recognized as a “signal” by a Signal Recognition Particle SRP, a proteinRNA complex o SRP attaches the translation complex to the RER and the growing peptide is “fed” into the center (cisternal space) of the RER The “signal” is clipped off What about other destinations in the cell? o These proteins are made on “free” ribosomes, but again, the Nterminal amino acids target the protein to the right place after it is made Mutations A heritable change in a gene = DNA Can be inherited by offspring or arises in a somatic cell o May or may not cause problems A mutagen is an agent (light, chemical, radiation) that causes mutations How do mutations occur? o 1. Errors can be made dur6ng DNA replication (wrong base pairs) Very rare ~1/10 o 2. Errors during repair Mutagens are agents that increase mutation frequency Famous mutation: Sickle Cell Anemia o Allele is called HBB GLU6VAL – the 6 amino acid is usually Glu but the mutation causes a substitution of Val o This DNA sequence = disease allele Point mutations: o Not chromosomal arrangements o NT substitutions: silent (often third base) o Missense (substitution of aa) o Nonsense (a stop codon is produced so premature termination of the protein) Nucleotide insertions or deletions will cause a frameshift, unless it’s 3 or multiples of 3 Stem Cells Undifferentiated cells with the potential to differentiate into multiple kinds of specialized cells What is the source of human embryonic stem cells = ES cells? o Embryos resulting from in vitro fertilization Zygote: the first, single cell formed by fusion of gametes Embryo: multicellular In Vitro Fertilization: o At the 8cell stage, one cell can be removed and tested for gender or for some genetic disease genes o Embryonic stem cells are harvested from hollow blastocysts (embryos of about 100 cells) about 56 days after IVF o There are about 30 cells in the inner cell mass 2 important properties of any usable stem cell: o 1. Can remain undifferentiated (unspecialized) in tissue culture and continue to divide = self renewal o 2. Have the potential to differentiate into specialized cells Not all stem cells are the same o Totipotent: every cell type is possible, up to generating a whole new individual Ex. Most plant cells, animal zygotes o Pluripotent: can differentiate into most cell types, but t produce a new individual o Multipotent: can differentiate into a specific set of possible cell types CHAPTER 18 Genes Gene: a segment of DNA that is transcribed to produce a functional RNA product: o mRNA that will be translated into protein o rRNA (part of ribosomes) o tRNA (dictionaries in translation) o Small noncoding (nc) RNAs Ex. Telomerase, RNA, snRNA, SRP RNA, microRNAs, etc. Bacteria: o Genes are clustered and transcribed together in operon, “Switched on” in response to an environmental signal o Operons: multiple gene, single promoter o Promoters: TATA box Lactose: o The repressor of transcription is inactivated, and RNA polymerase will bind to the promoter and transcribe all three genes in a polycistronic mRNA containing three start codons for three separate proteins Eukaryotes Eukaryotes: o Genes with similar functions are general NOT clustered Each gene has its own promoter Ex. No polycistronic mRNAs What determines whether a gene is expressed o Made into RNA and then a functional protein? Transcription is the biggie o Selection of promoters o But lots of other factors influence gene expression as well o Epigenetics 1. DNA can be methylated o Affects its expression o Involved in genomic imprinting, Xinactivation 2. Chromatin modification: o Histone proteins can be acetylated or methylated Increasingly appreciated as a major regulator of gene expression Transcription: o A typical eukaryotic gene has enhancers in addition to promoters o Transcription initiation in eukaryotes: A combination of transcription factors (proteins) will bind to promoters and enhancers Allows RNA polymerase to “load” onto a gene and begin transcription Enhancers: often tissuespecific, so whether or not a gene gets transcribed often will depend on whether the enhancerbinding transcription factors are present in a cell Alternative splicing: o Turning out to be more important than we thought >92% of human genes! Micro RNAs: o (miRNA, siRNA, RNAi) o Small noncoding (nc) that can interfere with gene expression by inhibiting translation or causing degradation of target mRNAs CHAPTER 19 – DEVELOPMENT Development Not all cells are the same Multicellular organisms are made of many kinds of cells o Organized into many tissues o Into many organs Differential gene expression Basic definitions of development: o Differentiation: cells become specialized Structurally and biochemically o Cell fate: final differentiated state of a cell o Determination: a cell has become committed to a cell fate Stem cells are NOT determined! o Morphogenesis: the creation of form The shape of an organism o Morphogen: a factor that influences morphogenesis o Transcription factors: proteins that bind DNA and influence transcription o Cytoplasmic determinants: factors that are asymmetrically distributed in the cytoplasm and influence development o Induction: process by which one cell influences the development of a neighboring cell Determination comes before differentiation Another important kind of transcription factor: o Homeotic genes discovered tin Drosophila encode transcription factors that determine the structures in different body segments Antennapedia mutant ^ The legs are where antennae should be How does one daughter cell become different from another? Figure 18.17a in textbook o 1. Something is asymmetric in the parent cell Ex. Cytoplasmic determinants Example of development controlled by cytoplasmic determinants: body plan in drosophila (fruit fly) Gene expressed in the mother are important in establishing axes = maternal effect genes It was known that there was some important factor I the egg cytoplasm that determined anterior organs o = Bicoid, a transcription factor and a Morphogen o 2. Another way to make 2 daughter cells depends on their relative positions A neighboring cell may emit signals differently to one daughter cell that will influence its cell fate = induction A cellcell signaling during development Example: stem cell connection o Inject the undifferentiated stem cells into an organism and let the other cells within the body cause the stem cells to differentiate by induction Just like in normal development An important discovery in nematodes: o Cell suicide = apoptosis = programmed cell death Morphogenesis via Apoptosis Controlled suicide of cells is regulated by cellcell signaling Nucleus condenses and DNA is fragmented Proteases are released to degrade proteins Mitochondria membrane leaks – releases cytochrome C CHAPTER 19 – CANCER Concepts Some viruses can cause cancer, but… o Most cancers are caused by mutations in genomes of somatic cells o More rarely, these mutations occur in cells that will produce gametes, cancer can then be inherited o The two basic types of cancer genes are Tumor suppressor genes, which normally suppress the cell cycle and oncogenes, which normally promote the cycle o Multiple mutations are found in most kinds of cancer Cancer Can cancer be contagious? (Caused by an infection pathogen)? o Yes o About 15% of human cancers are genital warts Caused by viruses that cause transcription of cancercausing genes o Good news: There is now a good vaccine against the most widespread Human Papilloma Virus HPV 85% of cancer is caused by mutations in genes loss of cell division control Most of the time, the mutation occurs in somatic cells (most cancer is NOT inherited) = sporadic o Due to accumulation of mutations in somatic cells over time Inherited cancer: one of the 2 homologous genes is already mutated in gametes o = The first mutational “hit” (mutation) is already present at birth o The second “hit” sometimes called “loss of heterozygosity” can occur due to another mutation, a deletion, or epigenetic silencing, resulting in cancer at a younger age 2 types of genes in the onset of cancer: o 1. Oncogenes: The normal, nonmutated version is called “protooncogene” Their function is to promote cell division/growth; the “gas pedal” of the cell cycle (like growth factors) Oncogenes are identified as DOMINANT mutations in protooncogenes (gas pedal gets stuck) Famous oncogenes: ras o How can normal protooncogenes mutate into oncogenes? Basically, 2 ways: This figure will be on the test! Overexpression by transposition/translocation, amplification or point mutation New (hyper) activity – the last one on the right o 2. Tumor Suppressor Genes: Normal versions of these genes function to inhibit cell division = “brakes” on the cell cycle Cell cycle checkpoints Recessive mutations – no gene product or dysfunctional gene product = “loss of function” “Knock out” – brakes fail In order to see effect, BOTH alleles must be mutated = Loss of Heterozygosity = LOH Famous suppressor gene: p53 What is happening at the molecular level in the progression of cancer? o Multiple mutations o Figure 18.26 in textbook The next mutation may be in a more “general” protooncogene like ras (in about 25% of all human tumors) or loss of a “general” tumor suppressor gene like p53 or RB (in about 50% of all human tumors) Last Lines of Defense Even if a cell acquires a series of mutations in cancer genes, DNA damage or other factors can trigger cell suicide (apoptosis) If the cell escapes death by suicide, there is normally still a “shutoff” system for cell division = shortening of telomeres causes cells to senesce (age, including not dividing) after 2060 divisions Other issues: o A. Tumor size is limited unless blood vessels develop in tumor – exciting progress in angiogenesis (Blood vessel development) inhibitors for solid tumors o B. Metastasis cannot occur unless tumors are able to leave the original site and colonize other parts of the body CHAPTER 20 – DNA Tools and Biotechnology Recombinant DNA started with the discovery of 2 important things: o 1. Small circular DNA molecules called plasmids that replicate in bacterial cells o 2. Enzymes that cut doublestranded DNA at specific DNA sequences = restriction enzymes These, along with the enzyme DNA ligase, make it possible to recombine DNA molecules in the lab What is recombinant DNA? o Two molecules of DNA The vector DNA and the insert DNA o Then those 2 are combined A vector DNA can replicate in bacterial cells o = A smaller circular plasmid or viral DNA Vector DNAs all have three things: o 1. A bacterial replication origin o 2. A cloning site for the insert DNA o 3. A gene called a “selectable marker” that allows bacteria to grow only if they contain the vector Ex. A gene that allows growth on an antibiotic The insert DNA can be from any kind of organism o Bacteria, plants, humans, or jellyfish Making the DNA A restriction enzyme makes a “staggered” cut in the vector DNA, producing small regions of single strands that can basepair with their complementary sequences = sticky ends The insert DNA is cut with the same restriction enzyme, so it has the same sticky ends The 2 DNAs are mixed, and the DNA Ligase covalently joins the two DNA molecules together, making a recombinant DNA molecule Next step is to multiply the cells… Getting the Recombinant DNA into Cells Transformation (like in lab with pGLO) Recombinant DNA is mixed with treated bacterial cells and the DNA will be taken up into some of the cells Selection: only cells that have received a plasmid can grow in the presence of the antibiotic, because the plasmid contains a gene encoding for antibiotic resistance The recombinant DNA is replicated many times in the bacterial cells – a DNA molecule has been cloned Figure 20.5 is important: Proteins = pharmaceuticals, antigens for vaccines DNA = analyze sequences, make GMOs, etc. Recombinant DNA molecules can be introduced into organisms, from bacteria to plants and animals Organisms that have received a recombinant DNA are called genetically modified organisms o GMOs o Dolly was a cloned organism, but not a GMO Are we making transgenic humans? o In a way – gene therapy is a transient (so far) kind of genetic modification o Diseases where gene therapy is being used: Bubble boy (ADA) – the hard part is introducing the DNA into the affected cells CHAPTER 21 – Genomes Genome Sequencing A genome includes all of the DNA sequences in an organism including all chromosomes o 2,000 – 4,000 genes in bacteria o 20,000 – 40,000 genes in multicellular eukaryotes Including us The Human Genome: What’s In It? Transposable Elements Transposons: o Transposable elements (“jumping genes”, transposons) were first described by Barbara McClintock working with corn in the 1940’s o Occur in all major life forms, from bacteria to man Make up about half of a genome “Regular” DNA transposons: Human genome: o More “junk” DNA o Simple sequence repeats (SSRs) of 113 bases Also called microsatellite DNA or STRs These are not what are used in CODIS forensics because their numbers vary so much in the human population o ~ 19,000 pseudogenes (mutated nonfunctional genes, evolutionary vestiges) and other non coding sequences CHAPTER 22 – Darwinian Evolution Major Misconceptions 1. Evolution is “just a theory” o In science a “best guess” is called a hypothesis o A theory is a unifying concept that explains many observations (data); atomic, gravitational, cell, chromosomal o Good theories withstand multiple tests, but… All theories must be falsifiable Theories are always subject to modification 2. Evolution is about the origins of life o Darwin’s theory of evolution describes how changes occur AFTER complex life arose 3. Evolution means atheism o Religion and science are 2 very different and important ways to understand life 4. “Survival of the fittest” o Evolution justifies the abuse of “weaker” human beings or animals by the “stronger” humans Sometimes called Social Darwinism 5 General Lines of Evidence in Favor of Darwinian Evolution 1. Biogeography = the geographical distribution of species o How it supports evolution: species on the same eland mass or nearby land masses are more similar to each other than those on different land masses Even if the environment is very similar o Darwin noticed that the fossils of South America were similar to the extant species nearby o Ex. Sugar glider (Australia) and flying squirrels (North America) o Examples of convergent evolution Similar structures of unrelated species 2. The fossil record = fossils are any preserved remnant of a life form o It takes unusual circumstances for a fossil to form o Something has to interfere with the normal process of decomposition 3. Comparative Morphology = it is possible to identify “homologous structures” which are signs of evolution and can identify common ancestry and adaptation o The notion of evolution as “tinkerer” 4. Molecular Biology = by comparing gene sequences, a lineage of ancestors will often become clear, with smaller differences seen between more closely related organisms o Mitochondrial DNA sequences have been especially useful as a “molecular clock” for describing the divergence of species in animals o Plants: chloroplast DNA sequences are used o Now, we are able to compare entire genomic sequences 5. Direct observation = example: rapid evolution of drug (methicillin) o Resistance = MRSA o Genetics problem set 2 – think about it Experiment: Pools in Trinidad: Guppies with spots attract more mates but also attract predators In the new pool there is a less aggressive predator o Does coloration change? o The transplanted population has an increase in the number of spots What about humans? o We did not descend from apes o We have a common ancestor that existed 5 million years ago Stem Cells What you need to know: o 2 ways to get stem cells to differentiate o Stems cells in regenerative medicine o Stem cells in research How to get stem cells to differentiate: o 1. Get embryonic stem cells to grow and then differentiate in culture Different treatments with small peptide growth factors cause the cells to divide and differentiate Remember cell division and cell communication and induction o 2. Inject the undifferentiated stem cells into an organism and let the other cells within the body cause the embryonic stem cells to differentiate by induction, just like in normal development How can we use stem cells? o Regenerative medicine: or cellbased medicine to replace dead or injured cells o Degenerative diseases: Parkinson’s Diabetes Osteoarthritis Blindness o Injuries: Heart disease Stroke Spinal cord injuries Burns Damage due to disease: o Parkinson’s disease: Tremor due to loss of dopamineproducing neurons Prevalence of Parkinson’s: ~ 1 million people in North America Janet Reno, Muhammad Ali, Michael J. Fox Dopamine is a neurotransmitter derived from tyrosine, an amino acid – produced by specific neurons in the substantia nigra region of the brain Involved in motor control and pleasure detection o Blindness (macular degeneration): Photoreceptor cell loss often results in irreversible blindness Cells committed to becoming rod precursors (determined) can be transplanted into damaged eye to reverse human blindness Damage due to injury: o Rebuilding the heart During heart attacks, muscle is deprived of oxygen Leads to cell death (a literal broken heart) o Affects 5 million Americans every year Injection of stem cells may allow regrowth of heart tissue Stem cell snake oil: o Some doctors and naturopaths are trying to sell stem cell therapy that is unproven and not approved by the FDA o Some “Stem Cell Clinics” are using liposuction to purify adult stem cells from patients and then injecting them intravenously back into the patient the same day for $6,000 $20,000 Use of stem cells in research: o Can make iPCs from people with a genetic disease including neurodegenerative diseases Including Alzheimer’s Including making human cell models of genetic diseases Can use for drug discovery Evolution of Populations Populations, not individuals, are the smallest biological unit that can evolve o Individuals cannot evolve What Darwin was missing: o The rules of inheritance In the 1940’s, a “modern synthesis” of Darwinian evolution with genetics occurred o Specifically, genetics as applied to populations Populations: a localized group of freely interbreeding individuals of the same species Species: we are going to use the Biological Species Concept: o = a group that freely interbreeds and produces fertile offspring in a natural setting and is reproductively isolated from other groups All human beings are the SAME species = homo sapiens Important terms: o Gene: a segment of DNA that encodes a functional protein or functional RNA product o Allele: different versions = variants of genes (wildtype, dominant, recessive, mutant) = different DNA sequences o Gene pool: ALL of the alleles of ALL of the genes of ALL of the individuals in a population Changes in gene pool = changes in allele frequencies = microevolution Mutations produce genetic variability o New alleles and phenotypes o The raw material for natural selection They occur randomly and DO NOT result from changes in the environment o Most mutations are deleterious (a gene becomes dysfunctional) but rarely a mutation can be beneficial and, if carried in gametes, can become established in a population Population Genetics Pop Gen Not like Mendelian genetics In a population, you need to figure out frequencies of alleles How can we figure out allele frequencies in a population? o If the population is not evolving, we can use a simple equation called HardyWeinberg equilibrium One important assumption of HardyWeinberg is that matings are random Any egg can fuse with any sperm o p = frequency of one allele in the population o q = frequency of another allele in the population o If there re only 2 possible alleles, sum of their frequencies must equal 1: p + q = 1 100% of the possible allele types Allele frequency: one letter (p or q) Genotype frequency: pg or qq = or pp p In a nonevolving population with only 2 possible alleles, what are the possible genotypes? o HardyWeinberg equation: p + 2pq + q = 1 R R R W W W C C , C C , C C Or AA, Aa, aa HardyWeinberg only applies to populations that are at equilibrium o Not changing, not evolving o Allele frequencies do not change What kind of factors could take a population OUT of equilibrium (genetically, this means that allele frequencies ARE changing)? Changes in a gene pool = microevolution 3 Causes of Microevolution 1. Genetic Drift: o If a population becomes too small, the gene pool decreases o Random fluctuations in mating can skew the relative frequencies of alleles Even resulting in the loss of alleles o What can cause a sudden decrease in a gene pool? Bottlenecks = due to near extinction Some catastrophe causes harm to the population Another form of bottleneck is domestication: as we breed for certain traits, we lose other traits The Founder Effect = isolation of a small group by emigration Genetic variability helps a population survive changes to its environment 2. Gene Flow: o Introduction of new alleles, for example, by immigration Increases the gene pool 3. Natural Selection: o If environmental factors allow some genotypes to survive and reproduce better than others, natural selection is at work and allele frequencies will change in a population o So the gene pool will decrease Remaining alleles are adaptive Increases the fitness of a population Survival + reproductive success = fitness o Sexual selection: Intrasexual = fighting for mates Intersexual = mate choice Species Microevolution = changing the composition of alleles within a population Macroevolution = the origin of new groups, such as species, genera, families, etc. o Includes mass extinctions and speciation Speciation = formation of a new species Biological Species Concept: o A group that freely interbreeds and produces fertile offspring in a natural setting and is reproductively isolated from other groups Reproductive Barriers Cause reproductive isolation Prezygotic = gametes do NOT fuse Postzygotic = gametes fuse to make zygotes but the offspring does not survive or is sterile 1. Prezygotic barriers: o Habitat o Temporal o Behavioral o Mechanical o Gametic 2. Postzygotic barriers: o Reduced hybrid viability Hybrids between species do not survive or are frail o Hybrid breakdown First hybrid generation is fertile but subsequent ones are not o Reduced hybrid fertility Hybrids are often sterile Mules Speciation How do new species arise from previously existing ones? o 2 ways: Either groups become geographically separated from each other (allopatric “other homeland”) or New species arise within the same original group at the same location (sympatric “same homeland”) o Allopatric speciation: An original group becomes separated by formation of geographical barriers or by migration of a splinter group Peripheral isolate o Sympatric speciation: New species can arise within an original population at the same location Especially well documented in plants, where it has been shown that polyploidy can occur due to hybridization to form a new species in a single generation
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