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Unit 4 What is evolution and how does it relate to species? If all of the cells in an organism have the same DNA, why and how are they different? The Structure of the Genetic Material DNA and RNA are ______________________ of ___________________________ Nucleic acids are _________________________ made of long chains of ____________________ monomers DNA and RNA are identical except for two things ____________________ bases DNA: RNA: _________________________ DNA: RNA: DNA is a ______________________________________ Helix James Watson and Francis Crick worked out the three-dimensional structure of DNA, based on X-ray crystallography by __________________________________ DNA consists of two polynucleotide strands wrapped around each other in a double helix _______________________________ backbones are on the outside and nitrogenous bases on the inside Each base pairs with a complementary partner creating h-bonds ___ with ___, and ___ with ___ DNA Replication DNA Replication Depends on Specific Base Pairing The Watson-Crick model of DNA structure suggested a mechanism for its replication DNA strands separate Enzymes use each strand as a ___________________ to assemble new nucleotides into complementary strands The mechanism of DNA replication is ___________________________________ Each new double helix consists of one _________ and one __________ strand DNA Replication: A Closer Look DNA replication begins at specific sites (________________________________) on the double helix Proteins _________________ and _______________________ the strands Replication proceeds in both _______________________, creating replication _______________ Parent strands open, daughter strands elongate Replication occurs _____________________________ at many sites Many Proteins Work Together in DNA Replicaiton and Repair At the end of each replication bubble is a __________________________, a Y-shaped region where new DNA strands are elongating _________________________ are enzymes that untwist the double helix at the replication forks Single-strand binding proteins _______________ to and _______________________ single-stranded DNA ______________________________ corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands _____________________________ cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the _____ end The initial nucleotide strand is a short RNA _________________________ An enzyme called __________________ can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand 3? DNA's sugar-phosphate backbones are oriented in opposite directions (___________________) Therefore when new nucleotides are added they can only be added from the ___ end of the parental DNA strand Once the RNA primer is produced by _____________________ Enzymes called ____________________________ catalyze the elongation of new DNA at a replication fork Most DNA polymerases require a _________ and a DNA ________________ strand The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells Along one template strand of DNA, the DNA polymerase synthesizes a ___________________ continuously, moving toward the replication fork To elongate the other new strand, called the _______________________, DNA polymerase must work in the direction away from the replication fork The lagging strand is synthesized as a series of segments called ________________ fragments, which are joined together by DNA _____________________ Proofreading and Repairing DNA DNA polymerases proofread newly made DNA, replacing any _____________________ nucleotides In ________________________________ of DNA, repair enzymes correct errors in base pairing DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo _______________________ changes In nucleotide excision repair, a _________________ cuts out and replaces damaged stretches of DNA From Gene to Protein The Flow of Genetic Information The information content of DNA is in the form of specific ____________________ of nucleotides The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins __________________ are the ______________ between genotype and phenotype Gene expression, Basic Principles of Transcription and Translation ___________ is the bridge between genes and the proteins for which they code ___________________________ is the synthesis of RNA under the direction of DNA Transcription produces _________________________ (________) _________________________ is the synthesis of a polypeptide, using information in the mRNA __________________________ are the sites of translation The central dogma is the concept that cells are governed by a cellular chain of command: ____________ ______________ _______________ The Genetic Code How are the instructions for assembling amino acids into proteins encoded into DNA? There are ____ amino acids, but there are only ________ nucleotide bases in DNA How many nucleotides correspond to an amino acid? Genetic information written in _____________________ is translated into amino acid sequences Nucleotide monomers represent letters in an alphabet that can form words in a language _______________ code The genetic code is the Rosetta stone of life The genetic code specifies the correspondence between RNA ________________ and _____________ in proteins Includes start and stop __________________ Nearly all organisms use exactly the same genetic code Now let’s look at Transcription and Translation in a little more detail. Transcription is the DNA-Directed Synthesis of RNA: A Closer Look Transcription is the first stage of ___________________________________ Molecular Components of Transcription RNA synthesis is catalyzed by _______________________, which pries the DNA strands apart and hooks together the RNA nucleotides The RNA is ______________________ to the DNA template strand RNA synthesis follows the same base-pairing rules as DNA, except that _________________ substitutes for _____________________ For example what would be the compliment of the following DNA template? 3’ C C G T T A A T A C G C G T A 5’ The DNA sequence where RNA polymerase attaches is called the _____________________; in bacteria, the sequence signaling the end of transcription is called the ____________________ The stretch of DNA that is transcribed is called a ___________________________________ Eukaryotic Cells Modify RNA After Transcription Enzymes in the eukaryotic nucleus modify pre-mRNA (_____________________________) before the genetic messages are dispatched to the cytoplasm During RNA processing, _______________ ends of the primary transcript are usually altered Also, usually some interior parts of the molecule are cut out, and the other parts spliced together Alteration of mRNA Ends Each end of a pre-mRNA molecule is modified in a particular way The 5 end receives a modified nucleotide ________________________ The 3 end gets a ______________________ These modifications share several functions They seem to facilitate the ________________________ of mRNA They _________________________ mRNA from hydrolytic enzymes They help ribosomes ___________________ to the 5 end Split Genes and RNA Splicing Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions These noncoding regions are called intervening sequences, or _______________________ The other regions are called ________________ because they are eventually expressed, usually translated into amino acid sequences _______________________________ removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence In some cases, RNA splicing is carried out by _________________________ _______________________________ consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites Translation is the RNA-Directed Synthesis of a Polypeptide: A Closer Look Genetic information flows from ___________ to ______________ through the process of _______________________ Molecular Components of Translation A cell translates an mRNA message into protein with the help of ____________ RNA (________) tRNA transfer ______________________________ to the growing polypeptide in a ribosome by matching the right amino acid to the correct _________________________ on ______ How? tRNA is a twisted and folded single strand of RNA ____________________ loop at one end recognizes a particular mRNA codon by base pairing Amino acid _____________________________________ is at the other end Each amino acid is joined to the correct tRNA by a specific ____________________ Ribosomes Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis The two ribosomal subunits (_______________ and ____________) are made of proteins and __________________ RNA (___________) A ribosome has three binding sites for tRNA The ____________ holds the tRNA that carries the growing polypeptide chain The ____________ holds the tRNA that carries the next amino acid to be added to the chain The ____________ is the exit site, where discharged tRNAs leave the ribosome Building a Polypeptide The three stages of translation Initiation of Translation The initiation stage of translation ___________ together _____________, a tRNA with the first amino acid, and the two ribosomal subunits First, a small ribosomal subunit binds with mRNA and a special _________________ tRNA Then the small subunit moves along the mRNA until it reaches the start ________________ (AUG) Proteins called initiation factors bring in the _____________ subunit that completes the translation initiation complex Elongation During the elongation stage, amino acids are __________________ one by one to the preceding amino acid at the C-terminus of the growing chain Each addition involves proteins called elongation factors and occurs in three steps: Termination of Translation Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome The A site accepts a protein called a release factor The release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide, and the translation assembly then comes apart What exactly is evolution? Descent with Modification: A Darwinian View of Life In 1859, Darwin published ______________________________________________________, presenting a strong, logical explanation of _______________________________________, _________________________ by the mechanism of ____________________________ How did he come up with this way of thinking? The Darwinian revolution challenged traditional views of a ____________ Earth inhabited by ___________________________ species Darwin’s ideas had deep historical roots Pre Darwinian Ideology The Greek philosopher ____________________ viewed species as fixed and arranged them on a ______________________________ A scale of increasing complexity The Old Testament holds that species were individually designed by ________ and therefore ___________________ In the century prior to Darwin, the study of ________________ revealed some potential changes to this ideology Ideas About Change over Time The study of _________________ helped to lay the groundwork for Darwin’s ideas Fossils are remains or traces of organisms from the past, usually found in sedimentary rock, which appears in layers or _______________________ ____________________________, the study of fossils, was largely developed by French scientist Georges Cuvier Cuvier advocated _______________________, speculating that each boundary between strata represents a catastrophe Geologists James Hutton and Charles Lyell perceived that changes in Earth’s surface can result from slow continuous actions still operating ___________________ Lyell’s principle of ______________________________ states that the mechanisms of change are constant over time This view strongly influenced Darwin’s thinking More Ideas About Change over Time ________________________________________ suggested that life on Earth evolves His mechanism included: Use and disuse of body _____________________________ Inheritance of acquired characteristics Mechanism didn’t truly prove evolution! Darwin’s Research As a boy and into adulthood, ______________________________ had a consuming interest in nature Darwin first studied medicine (unsuccessfully), and then theology at Cambridge University After graduating, he took an unpaid position as naturalist and companion to Captain Robert FitzRoy for a 5-year around the world voyage on the _________________________ The Voyage of the Beagle During his travels on the Beagle, Darwin collected specimens of South American plants and animals He observed that ________________________ resembled living species from the same region, and living species resembled other species from nearby regions He experienced an earthquake in Chile and observed the uplift of rocks Darwin was influenced by Lyell’s Principles of ____________________ and thought that the earth was more than 6000 years old His interest in geographic distribution of species was kindled by a stop at the ____________________ Islands west of South America He hypothesized that species from South America had colonized the Galápagos and _______________ on the islands Darwin’s Focus on Adaptation In reassessing his observations, Darwin perceived _________________________ to the environment and the origin of new species as closely related processes From studies made years after Darwin’s voyage, biologists have concluded that this is what happened to the Galápagos finches In 1844, Darwin wrote an essay on ______________________________ as the mechanism of ______________________________, but did not introduce his theory publicly Natural selection is a process in which individuals with favorable inherited traits are more likely to ______________________ and _______________________________ In June 1858, Darwin received a manuscript from ________________________________________, who had developed a theory of natural selection similar to Darwin’s Darwin quickly finished The _________________________________ and published it the next year The Origin of Species Darwin explained three broad observations: Descent with Modification Darwin never used the word ____________________ in the first edition of The Origin of Species The phrase ________________________________________ summarized Darwin’s perception of the unity of life The phrase refers to the view that all organisms are related through descent from an ancestor that lived in the remote past In the Darwinian view, the history of life is like a tree with branches representing life’s diversity Darwin’s theory meshed well with the hierarchy of ____________________________Who is Linnaeus? Carolus Linnaeus developed the ________________________________ of naming organisms using physical characteristics ___________________________ is the branch of biology that names and classifies species and groups them into broader categories Artificial Selection, Natural Selection, and Adaptation Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called ____________________________________ Darwin drew two inferences from two observations Observation #1: Members of a population often __________________ in their inherited traits Observation #2: All species can produce ___________ offspring than the environment can support, and many of these offspring ________________ to survive and reproduce Inference #1: Individuals whose inherited traits give them a ________________ probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals Inference #2: This unequal ability of individuals to survive and reproduce will lead to the ____________________________ of favorable traits in the population over generations Darwin was influenced by _____________________________, who noted the potential for human population to increase faster than food supplies and other resources If some heritable traits are advantageous, these will accumulate in a population over time, and this will ____________________________ the frequency of individuals with these traits This process explains the ____________________ between organisms and their environment Natural Selection: A Summary Individuals with certain _________________________ characteristics survive and reproduce at a higher rate than other individuals Natural selection increases the ______________________ of organisms to their environment over time If an environment changes over time, natural selection ____________ result in adaptation to these new conditions and may give rise to new species Note that _______________________ do not evolve; _____________________ evolve over time Natural selection can only increase or decrease heritable traits that _____________ in a population Evolution is not ___________ directed and does not lead to _____________________; adaptations vary with different environments and as environments change What is an adaptation? ____________________________ adaptations ____________________________ adaptations ____________________________ adaptations ____________________________ adaptations Will natural selection act on variation in hair style in a human population? Will natural selection act on tongue rolling in a human population? (Note: Tongue rolling is an inherited trait, caused by a dominant allele) Is the Green Heron population evolving if we only observe just one individual exhibiting this fishing behavior? Evolution is supported by an overwhelming amount of scientific evidence New discoveries continue to fill the gaps identified by Darwin in The Origin of Species Direct Observations of Evolutionary Change Two examples provide evidence for natural selection: natural selection in response to introduced plant species, and the evolution of drug-resistant bacteria Natural Selection in Response to Introduced Plant Species Soapberry bugs use their “beak” to feed on seeds within fruits In southern Florida soapberry bugs feed on balloon vine with larger fruit; they have longer beaks In central Florida they feed on goldenrain tree with smaller fruit; they have shorter beaks Correlation between fruit size and beak size has also been observed in Louisiana, Oklahoma, and Australia In all cases, beak size has evolved in populations that feed on introduced plants with fruits that are smaller or larger than the native fruits These cases are examples of evolution by natural selection In Florida this evolution in beak size occurred in less than 35 years The Evolution of Drug-Resistant Bacteria The bacterium Staphylococcus aureus is commonly found on people One strain, methicillin-resistant S. aureus (MRSA) is a dangerous pathogen S. aureus became resistant to penicillin in 1945, two years after it was first widely used S. aureus became resistant to methicillin in 1961, two years after it was first widely used Methicillin works by inhibiting a protein used by bacteria in their cell walls MRSA bacteria use a different protein in their cell walls When exposed to methicillin, MRSA strains are more likely to survive and reproduce than nonresistant S. aureus strains MRSA strains are now resistant to many antibiotics The study of fossils provides strong evidence for evolution The fossil record shows that organisms have evolved in a historical _________________________ The oldest known fossils are _________________________________ cells The oldest eukaryotic fossils are a billion years ________________________ What are Fossils? Fossils can document important _____________________________ For example, the transition from land to sea in the ancestors of cetaceans A mass of other evidence reinforces the evolutionary view of life _______________________________, the geographic distribution of species, suggested to Darwin that organisms evolve from common ancestors Darwin noted that animals on islands resemble species on nearby mainland more closely than they resemble animals on similar islands close to other __________________________ Comparative Anatomy Comparative anatomy is Homology is Comparative embryology is Many vertebrates have common embryonic structures, revealing homologies When you were an embryo, you had a tail and pharyngeal pouches (just like an embryonic fish) Some homologous structures are _________________________________ organs For example, the pelvic and hind-leg bones of some modern whales Homologies and “Tree Thinking” ______________________________________ can be made using different types of data, for example, anatomical and DNA sequence data Homologies form nested patterns in ____________________________________ Evolutionary trees can be made using different types of data, for example, ________________________ and _________ sequence data Molecular biology: All living things share a common DNA code for the proteins found in living cells We share genes with bacteria, yeast, and fruit flies A Different Cause of Resemblance: Convergent Evolution ________________________ evolution is the evolution of similar, or __________________________, features in distantly related groups ________________________ traits arise when groups independently adapt to similar environments in similar ways Convergent evolution does not provide information about __________________________ What are the Processes for Evolutionary Change? The Evolution of Populations What is the Unit of Evolution? One misconception is that organisms ________________ during their lifetimes Natural selection acts on individuals, but only __________________________ evolve For example, a population of medium ground finches on Daphne Major Island What happened to the population? During a drought, average beak depth increased Why? Larger beaks were more likely to crack large seeds and survive while smaller beaks could not Therefore the finch population evolved by natural selection What was needed for evolution to occur? ___________________________________ The birds could not just grow larger beaks you either had a large beak or not Genetic variation makes evolution possible Variation in heritable traits is a _______________________________ for evolution What is Genetic Variation? Genetic Variation Genetic variation among individuals is caused by differences in _______ or other _____ segments _____________________ is the product of inherited genotype and environmental influences Are these two different species of caterpillar? Natural selection can _____________ act on variation with a genetic component Sources of Genetic Variation __________________________, or changes in the nucleotide sequence of DNA, is the ultimate source of new alleles Not all mutations are harmful they can also be ______________ or ________________ __________________________________________ is an important source of genetic variation If a gene is duplicated, the new copy can undergo mutation without affecting the function of the original copy For example, an early ancestor of mammals had a single gene for an olfactory receptor The gene has been duplicated many times, and humans now have 1,000 different olfactory receptor genes _____________________________________ shuffles alleles to produce new combinations Independent assortment of genes/chromosomes during meiosis Crossing over of homologous chromosomes during prophase I meiosis Further variation arises when sperm randomly unite with eggs in fertilization Populations are the units of evolution Let’s define some terms A population is Evolution is Biological Evolution? A _________________________ is the total collection of genes in a population at any one time ____________________________ is a change in allele frequencies in a population over generation Macroevolution? The Hardy-Weinberg equation can be used to test whether a population is evolving The _______________________________________________ states that allele and genotype frequencies within a sexually reproducing, diploid population will remain in equilibrium unless outside forces act to change those frequencies Imagine that there are two alleles in a blue-footed booby population: W and w What are the possible genotypes? Once the frequencies are calculated you can then test the same population again in the ______________. If the frequencies of your alleles are the same then there is no evolution occuring Remember The Hardy-Weinberg principle describes a population that is ____________ evolving For a population to remain in Hardy-Weinberg equilibrium for a specific trait, it must satisfy five conditions: Applying the Hardy-Weinberg Principle We can assume the locus that causes phenylketonuria (PKU) is in Hardy-Weinberg equilibrium given that: 1. The PKU gene mutation rate is _____________ 2. 3. 4. Mate selection is ____________ with respect to whether or not an individual is a carrier for the PKU allele Natural selection can only act on __________ homozygous individuals who do not follow dietary restrictions The population is __________________________ 5. Migration has _______ effect as many other populations have similar allele frequencies The occurrence of PKU is 1 per 10,000 births PKU is a autosomal recessive disease q2 0.0001 q 0.01 The frequency of normal alleles is p 1 – q 1 – 0.01 0.99 The frequency of carriers is 2pq 2 0.99 0.01 0.0198 or approximately 2% of the U.S. population What would cause microevolution to occur? Natural selection, genetic drift, and gene flow can alter allele frequencies in a population If the five conditions for the Hardy-Weinberg equilibrium are not met in a population, the population’s gene pool may _______________________ __________________________ are rare and random and have little effect on the gene pool If _______________________________________, allele frequencies won’t change much (although genotype frequencies may) Three main causes of evolutionary change _______________________________ If individuals _____________________ in their survival and reproductive success, natural selection ________________ alter allele frequencies Consider the boobies: Would webbed or nonwebbed boobies be more successful at swimming and capturing fish? _______________________________ The smaller a sample, the greater the chance of deviation from a predicted result ___________________________________ describes how allele frequencies fluctuate unpredictably from one generation to the next Genetic drift tends to ____________________ genetic variation through losses of alleles The ______________________________ leads to a loss of genetic diversity when a population is greatly ____________________ For example, the northern elephant seal was hunted to near extinction in the 1700s and 1800s Understanding the bottleneck effect can increase understanding of how human activity affects other species Case Study: Impact of Genetic Drift on the Greater Prairie Chicken Loss of prairie habitat caused a severe reduction in the population of greater prairie chickens in Illinois The surviving birds had low levels of genetic variation, and only 50% of their eggs hatched Researchers used DNA from museum specimens to compare genetic variation in the population before and after the bottleneck The results showed a loss of alleles at several loci Researchers introduced greater prairie chickens from population in other states and were successful in introducing new alleles and increasing the egg hatch rate to 90% Genetic drift produces the _________________________ when a few individuals colonize a new habitat The smaller the group, the more ____________________________ the gene pool of the new population will be from the gene pool of the original population Effects of Genetic Drift: A Summary 1. Genetic drift is significant in __________ populations 2. Genetic drift causes allele frequencies to change at ________________ 3. Genetic drift can lead to a _____________ of genetic variation within populations 4. Genetic drift can cause harmful alleles to become ______________ _______________________________ __________________________________ is the movement of individuals or gametes/spores between populations and can alter allele frequencies in a population Gene flow can ____________________ or _________________ the _____________ of a population For example Gene flow can _________________ the fitness of a population as exhibited in the great tit (Parus major) on the Dutch island of Vlieland _________________________ from the mainland introduces alleles that decrease fitness Natural selection ________________ for alleles that increase ________________ Birds in the central region with high immigration have a lower fitness; birds in the east with low immigration have a higher fitness Gene flow can _____________________ the fitness of a population Consider, for example, the spread of alleles for resistance to insecticides Insecticides have been used to target mosquitoes that carry West Nile virus and malaria Alleles have evolved in some populations that confer insecticide resistance to these mosquitoes The flow of insecticide resistance alleles into a population can cause an increase in fitness Of the three main causes for evolution which is the primary cause for evolution? ______________________________ is the only mechanism that consistently causes adaptive evolution Evolution by natural selection involves both _____________ and “_______________” New genetic variations arise by ________________ Beneficial alleles are “________________” and favored by ____________________________ Only natural selection consistently results in ______________________ evolution A Closer Look at Natural Selection Natural selection brings about adaptive evolution by acting on an organism’s phenotype Relative Fitness The phrases “struggle for existence” and “_____________________________________” are misleading as they imply direct competition among individuals __________________________ success is generally more subtle and depends on many factors Natural selection can alter variation in a population in three ways Stabilizing selection favors ___________________ phenotypes, acting against _______________ phenotypes Stabilizing selection is very common, especially when environments are _______________ Directional selection acts against individuals at one of the phenotypic _____________________ Directional selection is common during periods of environmental _______________________, or when a population ______________________ to a new and different habitat Disruptive selection favors individuals at both ______________________ of the phenotypic range This form of selection may occur in ________________________ habitats The Key Role of Natural Selection in Adaptive Evolution Striking adaptation have arisen by _________________________________ For example, the jaws of snakes allow them to swallow prey larger than their heads Natural selection increases the frequencies of alleles that enhance __________________ and _____________________ Adaptive evolution occurs as the match between an organism and its environment ________________ Because the environment can change, adaptive evolution is a _____________________ process Genetic drift and gene flow do not ________________________ lead to adaptive evolution as they can increase or decrease the match between an organism and its environment Sexual Selection Sexual selection is It can result in ___________________________________, marked differences between the sexes in secondary sexual characteristics _________________________________ competition is competition among individuals of one sex (often males) for mates of the opposite sex In ____________________________ competition often called mate choice, occurs when individuals of one sex (usually females) are choosy in selecting their mates Male _______________________________ due to mate choice can increase a male’s chances of attracting a female, while decreasing his chances of survival How do female preferences evolve? The good genes hypothesis suggests that if a trait is related to male health, both the male trait and female preference for that trait should _________________________ in frequency Frequency-Dependent Selection In ___________________________________, the fitness of a phenotype declines if it becomes too common in the population Selection can favor whichever phenotype is less common in a population For example, frequency-dependent selection selects for approximately equal numbers of “rightmouthed” and “left-mouthed” scale-eating fish Why Natural Selection Cannot Fashion Perfect Organisms 1. 2. 3. 4.