Bio213 Exam 2

Sexual selection

Acts on characters that determine reproductive success If an individual survives but does not reproduce, it makes no contribution to the next generation Sexual selection favors traits that increase the chances of reproduction

p= f(A)=

(# AA+ ½#Aa)/ Total population

In any population Frequency of allele A=p=

(# AA+ ½#Aa)/ Total population or 2Naa+NAa/2N Where N is the total number of individuals in the population

q=f(a)=

(#aa + ½#Aa)/ Total popultaion

In any population Frequency of allele a= q=

(#aa + ½#Aa)/ Total popultaion or 2Naa+NAa/ 2N Where N is the total number of individuals in the population

Evolutionary theory has many useful applications

- Development of vaccines; understanding and treating diseases - Developing better agricultural crops and industrial processes - Understanding the diversification of life and how species interact

New DNA can become part of a replicon in two ways:

- Inserted near an origin of replication in host chromosome - it can be part of a carrier sequence, or vector, that already has an origin of replication

Inserting the recombinant DNA into a cell:

- Make plasma membranes more permeable - Electroporation

If the Hardy-Weinberg conditions hold

Allele frequencies remain constant After one generation, genotype frequencies occur in these proportions: Genotype AA Aa aa Frequency p^2 2pq q^2

Four types of Transposons Retrotransposons

Also make RNA copies of themselves SINEs and LINEs are types of retrotransposons

Which statement correctly describes stem cells? Select one: -An embryonic stem cell is a cell in an organism that may divide indefinitely and has the ability to differentiate into different types of cells. -An adult stem cell is a cell that has the ability to give rise to an entire organism. -All types of stem cells can give rise to all the different types of cells in an organism. -Stem cells are cells that come from embryos. -Stem cells divide only into other stem cells.

An embryonic stem cell is a cell in an organism that may divide indefinitely and has the ability to differentiate into different types of cells.

The thale cress

Arabidopsis thaliana

Four types of Transposons DNA transposons

Are excised from the original location and become inserted at a new location without being replicated

Transposons (transposable elements)

Are moderately repetitive sequences

SINEs and LINEs

Are transcribed into RNA, which then cuts as a template for new DNA which is inserted at a new location

Restriction enzymes and DNA ligase

Are used to cut DNA into fragments and then splice them together in new combinations

Haplotype maps

Are used to identify SNPs that are linked to genes involved in disease

Selection

As selection acts on a trait, the frequency of the allele that codes for that trait increases in the next generation (so long as the trait is heritable)

Crop plants have been modified to produce their own insecticides

Bacillus thuringiensis B. Thuringiensis Toxin Reduced pesticide

Genomic library

Bacteria clones with many different fragments of a genome are called a genomic library

Bacterial cells Recombinant plasmid

Bacterial cells can contain hundreds of copies of a recombinant plasmid. The power of bacterial transformation to amplify a gene is extraordinary

Restriction Endonucleases

Bacterial enzymes used to cut DNA

Trade-off

Benefit must outweigh cost if an adaptation is to evolve; the trade-off must be worthwhile Conspicuous features used by some males to compete with other males are a trade-off with reproductive success

Hypothesis

Biologically functional recombinant chromosomes can be made in the laboratory

Biologists observation

Biologists have observed the processes and results of evolution, and accumulated evidence on how evolutionary change occur

Adaptations involve

Both fitness costs and benefits

The nematode

Caenorhabditis elegans

Galapagos Islands are a laboratory of evolution

Helped shape Darwin's original ideas Remain an important test venue for studies Long-term study on "darwin's finches": Break size changed following drought

Introducing new individuals into a small population is an example of ... Select one: -gene flow that will probably bring maladapted traits and harm the population. -gene flow that will increase genetic diversity and most likely help the population. -frequency-dependent selection, which should increase the common phenotypes present in the population. -interspecific competition. -frequency-dependent selection, which should decrease the common phenotypes present in the population.

gene flow that will increase genetic diversity and most likely help the population.

What term is used to describe all the alleles at every locus for all individuals within a population? Select one: heterozygotes gene pool selection fitness homozygotes

gene pool This answer is correct because the gene pool is the genetic variation present (all copies of every type of allele) in a population.

Rapid genotyping technologies are bing used to understand the

genetic basis of diseases such as diabetes, heart disease, and Alzheimer's disease

A forest fire kills 75% of a shrub population and 100% of the tall trees in an old-growth forest. After some time, the shrubs are much taller than those of a nearby population that was not affected by the fire. What evolutionary mechanism(s) could explain this difference? Select one: -gene flow from the neighboring population -selection for tall shrubs in the fire -increased competition for resources relative to the adjacent population -stabilizing selection and gene flow -genetic drift and/or directional selection

genetic drift and/or directional selection

Technologies to analyze SNPs include

rapid sequencing methods and DNA microarrays One aim is to correlate SNP-defined haplotypes with diseases

Nonrandom mating Sexual selection

A form of nonrandom mating that does change allele frequencies It often results in evolution of significant differences between males and females of a species

Several events could have occurred at any given nucleotide Multiple substitutions

More than one change at a given position

Molecular homologies

Mouse and fruit fly

p+q=

1

Fossilized bones are discovered. Carbon dating indicates that they contain one-fourth the normal amount of carbon-14 found in the bones of a living specimen. The half-life of carbon-14 is 5,730 years. Approximately how old are the bones? Select one: 12,000 years 4.5 billion years 4.5 million years 5,000 years 2,000 years

12,000 years

How often does DNA polymerase attach the wrong nucleotide? Select one: 1:100 1:100,000 1:1 1:100,000,000,000 never

1:100,000

What variable in the Hardy-Weinberg equation expresses the heterozygous genotype? Select one: q2 2 pq p2 p2 + q2 None of the answers are correct.

2 pq

The complete haploid human genome sequence was finished in

2005 Since then, the diploid genomes of several individuals have been sequenced and published

A population survey shows that 160 out of 250 individuals express the recessive phenotype. What percentage of the population would you predict to be heterozygotes? Select one: 20% 80% 32% 36% 64%

32% This answer is correct because if the recessive phenotype is determined by a homozygous recessive genotype, then: q2 = (160/250) = 0.64; therefore, q = 0.8. With q, solve for p: 1 - q = p or 1 - 0.8 = 0.2. To find the frequency of heterozygotes, use 2 pq: 2 pq = frequency of heterozygotes = 2(0.2)(0.8) = 0.32 or 32%.

Recombinant DNA

A DNA molecule made in the laboratory that is derived from at least two genetic sources

Expression vectors For prokaryotes

A bacterial promoter, a transcription termination signal, and a sequence for ribosome binding on the mRNA, must all be included

Genomic library

A genomic library is a collection of DNA fragments that comprise the genome of an organism The DNA is cut into fragments by restriction enzymes, and each fragment is inserted into a vector, which is used to produce a colony of recombinant cells

Population

A group of individuals of the same species that live and interbreed in a particular geographic area

Heritable Trait

A heritable trait is at least partly determined by genes

After the Beagle trip, Darwin read Thomas Malthus's An Essay on the Principle of Population (1798)

A limit to how many individuals can survive on limited resources (originally proposed for economies of human populations) Inspired Darwin's critical idea of natural selection favoring individuals with the highest fitness in a given environment

The nematode

A millimeter-long sold roundworm It has a transparent body made up of about 1,000 cells, yet has complex organ systems It has about 3.5 times as many protein-coding genes as do yeasts

Modern Synthesis

A new understanding of evolutionary biology emerged- the Modern Synthesis- with the advent of transmission and population genetics Biologists began to study mechanistic aspects of evolution as well as broad evolutionary patterns

Haplotype

A piece of chromosome with a set of SNPs that are usually inherited as a unit Analysis of human haplotypes have shown that there are at most 500,000 common variations

population evolves

A population evolves when individuals with different genotypes survive or reproduce at different rates

Inserting the recombinant DNA into a cell: Electroporation

A short electric shock creates temporary pores in membranes and DNA can enter

Nonsynonymous substitution

A substitution that does cause a change in the amino acid specified is a non synonymous substitution (or missense substitution) These are likely to be deleterious; but protein shape and function is not always altered, so it may be selectively neutral

Why would traits that make an individual more susceptible to predation and other costs be attractive to a potential mate? Fisherian Arbitrary Choice hypothesis

A trait becomes advantageous for arbitrary reasons and is passed on

Mutation rates are low

About one per locus in a million zygotes But it creates a lot of variation because of the large number of genes that can mutate, and because populations have large numbers of individuals

Plasmin

After wounds heal, blood clots are dissolved by plasmin. Plasmin is stored as an inactive form called plasminogen

Who independently formulated the hypothesis of natural selection before Darwin published his work? Select one: Charles Lyell Thomas Malthus Alfred Russel Wallace Jean Baptiste Lamarck Josiah Wedgewood

Alfred Russel Wallace

Which of the following is an accurate statement about microarrays? Select one: -Microarrays are a way to assess the expression of thousands of genes at one time. -Microarrays give a snapshot of gene expression at a given point in time and/or under specific experimental conditions. -Microarrays produce a large volume of background noise, which means very conservative analyses are necessary. - Investigations cannot end with microarray results; further analysis of gene function is also necessary. - All answers are accurate statements about microarrays.

All answers are accurate statements about microarrays.

In the linkage mapping process for the Human Genome Project, which of the following data types were useful? Select one: -short tandem repeats -restriction fragment length polymorphisms -gene sequences -polymorphisms -All answers are correct.

All answers are correct.

Which of the following is a potential application of information from -omics analyses? Select one: -understanding how microbes interact with hosts -identifying the species in microbial communities -sourcing a disease phenotype to a specific genetic mutation -comparing and contrasting global gene expression in different tissues -All answers are correct.

All answers are correct.

Which of the following is a problem with cloning animals? Select one: -The molecular process by which dedifferentiation takes place is not known. -Cloning organisms by somatic cell nuclear transfer is technically difficult and time-consuming. -At every step of cloning an organism by somatic cell nuclear transfer, there is a high rate of failure. -Cloned animals often die young. -All answers are correct.

All answers are correct.

Which of the following is a reason that a prokaryotic gene expression system might not be compatible for expressing eukaryotic genes? Select one: -Bacteria lack introns. -Bacteria lack splicing machinery. -Eukaryotic DNA includes introns. -Eukaryotic proteins often undergo additional processing after translation to become functional. -All answers are correct.

All answers are correct.

Which of the following statements are true regarding human cloning? Select one: -Most people think it is unethical to clone humans. -It is possible to use human embryos for therapeutic cloning. -The same cells that are used for therapeutic cloning can be used for reproductive cloning. -Induced pluripotent stem cells may circumvent the need for human embryos as a source of stem cells and the associated ethical issues. -All answers are correct.

All answers are correct.

All evolutionary innovations are ______

All evolutionary innovations are modifications of previously existing structures

What is the purpose of creating genetically modified food? Select one: -None of the answer choices are correct. -to produce crops that are resistant to herbicides -to produce crops that are resistant to pests -to enhance the nutritional or therapeutic value of food components -All of the answer choices are correct.

All of the answer choices are correct.

Genetic variation

Can affect an individual's response to a particular drug

TPA

Can be used to treat strokes and heart attacks, but large quantities are needed. Can be made using recombinant DNA technology

Sticky ends

Can bind by base pairing to other sticky ends Fragments from different sources can be joined Then ligase catalyzes formation of covalent bonds between adjacent nucleotides at fragment ends, joining them to form a s single, larger molecule

Insertion of a transposon at a new location

Can have important consequences, such as mutations and gene duplications They can result in shuffling the genetic material and creating new genes Transposons may have played a role in endosymbiosis

Transposons

Can insert into genes at random; the mutated bacteria are tested for growth and survival, and DNA is sequenced

M. genitalium

Can survive in the laboratory with only 382 functional genes Efforts are underway to make a synthetic genome based on M. genitalium- to create artificial life This could have many useful benefits, but also many ethical concerns

DNA ligase

Catalyzes the joining of DNA fragments

Evolution must work within the boundaries of universal constraints such as:

Cell size, constrained by surface area-to-volume ratios Protein folding, constrained by the types of bonding that can occur Laws of thermodynamics that constrain energy transfers Developmental processes also constrain evolution

Arabidopsis genes unique to plants

Cell wall and growth- 42 genes Water channels- 300 genes Photosynthesis- 139 genes Defense and metabolism- 94 genes

Inserting the recombinant DNA into a cell: Make plasma membranes more permeable

Cells may be treated with chemicals to make plasma membranes more permeable- DNA diffuses in

Universal genes

Certain genes are present in all organisms (universal genes); and some universal gene segments are present in many organisms This suggests that a minimal set of DNA sequences is common to all cells

Transitions

Changes between two purines or two pyrimidines

Alfred Russel Wallace Charles Lyell

Charles Lyell (a geologist friend of Darwin's) presented Wallace's paper together with excerpts from Darwin's unpublished 1844 essay to a scientific society in London Darwin fleshed out his theory to publish 'On the Origin of Species' in 1859

What have we learned from sequencing prokaryotic genomes?

Chlamydia trachomatis Rickettsia prowazekii Mycobacterium tuberculosis Streptomyces coelicolor E. Colie strain O157:H7 Sever acute respiratory syndrome (SARS)

Alfred Russel Wallace (1823-1913)

Co-founder of the theory of evolution by natural selection Darwin withheld publishing his controversial ideas until Wallace sent him a paper describing his own ideas of natural selection, which were nearly identical to his

In order to provide access to a new airport, a road was built through a previously undisturbed forest, which isolated a small group of deer from the rest of its population. After several years, conservation biologists determined that 75% of the individuals in the isolated population demonstrated a recessive phenotype that is rare in the rest of the population. How would you determine if this is due to inbreeding or genetic drift? Select one: -Determine if the population is in Hardy-Weinberg equilibrium. -Compare the number of heterozygotes to homozygotes over time. -Determine the fitness of the recessive phenotype. -Compare the selection coefficients in the two populations. -Determine the proportion of breeding individuals in the population.

Compare the number of heterozygotes to homozygotes over time.

Comparing gene sequences among species allows us...

Comparing gene sequences among species allows us to determine history and timing of synonymous and non synonymous substitutions This information can be mapped on a phylogenetic tree

Evolutionary changes are determined by

Comparing nucleotide or amino acid sequences among different organisms The longer two sequences have been evolving separately, the more differences they accumulate The timing of evolutionary changes can be determined and causes can be inferred

Concern over environmental effects

Concern over environmental effects centers on escape of transgenes into wild populations For example, if the gene for herbicide resistance made its way into the weed plants New super-weeds could develop from transgenic crops. For example, a drought tolerant crop plant might spread into, and upset the colony of, a desert Beneficial insects can also be killed from eating plants with B. Thuringiensis genes

Plasmin TPA

Conversion of plasminogen is activated by TPA

DNA synthesis

DNA can be synthesized by PCR if appropriate primers are available The amplified DNA can then be inserted into plasmids to create recombinant DNA and cloned in host cells

The Human Genome Project used two approaches: Shotgun sequencing continued

DNA fragments are sequenced using chemically modified nucleotides, dideoxynucleotides (ddNTPs) These are added by DNA polymerase to a polynucleotide chain but synthesis then stops because ddNTP has no hydroxyl group at the 3' position

Gel Electrophoresis

DNA fragments cut by enzymes can be separated by gel electrophoresis - A mixture of fragments is placed in a well in a semisolid gel and an electric field is applied across the gel - Negatively charged DNA fragments move towards positive end - Smaller fragments move faster than larger ones

Three additional ways of manipulating DNA DNA microarray

DNA microarray technology provides a large array of sequences for hybridization experiments A series of DNA sequences are attached to a glass slide in a precise order The slide has microscopic wells which each contain thousands of copies of sequences up to 20 nucleotides long

Three additional ways of manipulating DNA DNA microarrays continued

DNA microarrays can be used to identify specific single nucleotide polymorphisms or other mutations If mRNA is to be analyzed, it is usually incubated with reverse transcriptase to make cDNA Fluorescent dyes take the cDNAs and they are used to probe the DNA on the microarray

Scientists identified a SNP site associated with an increased risk of hypertension. How is this information used to diagnose people with a potential risk of hypertension? Select one: -DNA samples from a patient could be sequenced and analyzed for the presence of the SNP. -The SNP could be removed from the sample DNA and amplified using PCR. -DNA from the patient could be combined with sample DNA carrying the SNP. -The SNP could be inserted into a plasmid and injected into the patient. -None of the answers are correct.

DNA samples from a patient could be sequenced and analyzed for the presence of the SNP.

Artificial Selection

Darwin had also observed variation and artificial selection of certain desirable traits in plants and animals by breeders

Darwin Pigeons

Darwin himself bred pigeons. He recognized the close parallels between selection by breeders and selection in nature

Darwin

Darwin often went ashore to study rocks and collect specimens, and make observations about the natural world

Darwin Postulated

Darwin postulated that species had reached the islands from the mainland, but then had undergone different changes on different islands Part of the puzzle was determining what could be a mechanism for such changes

Sequence alignment technique

Deletions and insertions in the sequence that have occurred since the two species diverged are determined by adding gaps and aligning sequences Long sequences are aligned by computer algorithms A similarity matrix is constructed

Hardy-Weinberg equilibrium

Describes a model situation in which allele frequencies do not change; its like a null hypothesis or a starting point

Shotgun sequencing is used to

Detect presence of known microbes, as well as heretofore unidentified organisms

Sexual dimorphism

Differences between sexes

Alleles

Different forms of a gene

Several events could have occurred at any given nucleotide Coincident substitutions

Different substitutions in different descendants

Some Medically Useful Products of Biotechnology Tissuing plasminogen activator

Dissolves blood clots after heart attacks and strokes

Crop plants have been modified to produce their own insecticides B. Thuringiensis

Dried preparations of B. thuringiensis are sold as a safe alternative to synthetic insecticides. The toxin is easily biodegradable

The fruit fly

Drosophila melanogaster

Pseudogenes

Duplicates copies of genes that are no longer functional

Globin gene family

During development, different members of the global gene family are expressed at different times and in different tissues Hemoglobin of the human fetus contains y-globin, which binds O2 more tightly than adult hemoglobin

Method E. Coli

E. Coli plasmids carrying a gene for resistance to either the antibiotic kanamycin (K) or tetracycline (T) are cut with a restriction enzyme E. Coli plasmids are cut The cut plasmids are mixed with DNA ligase to form recombinant DNA The plasmids are inserted into E. coli

Efforts to define minimal genome

Efforts to define a minimal genome involve computer analysis of genomes, the study of the smallest known genome (M. genitalium), and using transposons as mutagens

Difference between sexes, sexual dimorphism, depends on investment of each sex in offspring Look alike

Equal investment in offspring and attractiveness

Gene families

Eukaryotes have closely related genes called gene families These arose over evolutionary time when different copies of genes underwent separate mutations For example: Genes encoding the globin proteins all arose from a single common ancestral gene

There are major differences between eukaryotic and prokaryotic genomes

Eukaryotic genomes are larger and have more protein-coding genes Eukaryotic genomes have more regulatory sequences. Greater complexity requires more regulation Much of eukaryotic DNA is noncoding, including introns, gene control sequences, and repeated sequences Eukaryotes have multiple chromosomes; each must have an origin of replication (ori), a centromere, and a telomeric sequence at each end

A revolutionary theory

Evolution by natural selection produces the variation and forms of life Testable scientific theory supported by overwhelming evidence

A revolutionary theory Clear case studies from throughout biology

Evolution off antibiotic resistance in pathogens Short and long-term observations on natural populations subject to variable conditions

Using Transposon Mutagenesis to Determine the minimal Genome Method

Experiment 1: insert inactive gene A Experiment 2: insert inactive gene B

Population genetics has three goals:

Explain the patterns and organization of genetic variation Explain the origin and maintenance of genetic variation Understand mechanisms that cause changes in allele frequencies

Expression vectors may also have: Tissue-specific promoters

Expressed only in certain tissues at certain times

Inference of outcomes of natural selection

Favored traits accumulate and lead to changes through time Over time populations adapt to their environment and become more able to cope with their environment

Natural selection can act on characters with quantitative variation in three ways: Directional selection

Favors individuals that vary in one direction Moves towards the low end of the bell curve Mean goes down Graph shifts left

Natural selection can act on characters with quantitative variation in three ways: Disruptive selection

Favors individuals that vary in opposite directions from the mean Two extremes have a higher fitness than the mean value Causes curve to become bimodal= two modes

Characters

Features of a phenotype are the characters (e.g. eye color)

Difference between sexes, sexual dimorphism, depends on investment of each sex in offspring Pretty males

Females invest more in offspring Males invest more in attractiveness

For a population to evolve, it members...

For a population to evolve, its members must posses heritable genetic variation

Genetic structure

Frequencies of different alleles at each locus and frequencies of genotypes in a Mendelian population make up the genetic structure of the population

What have we learned from sequencing prokaryotic genomes? Functional genomics

Functional genomics assigns functions to the products of genes H. influenze chromsome has 1,738 open reading frames. When it was first sequenced, only 58% coded for proteins with known functions Since then the roles of many other proteins have been identified

Gene cloning

Gene cloning is now used to produce proteins in large amounts Almost any gene can be inserted into bacteria or yeasts, and the resulting cells induced to make large quantities of the product Requires specialized vectors

DNA fragments used for cloning come from four sources:

Gene libraries Reverse transcription from mRNA Products of PCR Artificial synthesis or mutation of DNA

Genes Color coded

Genes are color coded based on the metabolic processes they are involved in

Evolution of nucleic acids and proteins depends on mutations

Genes can evolve by nucleotide substitutions, which can result in amino acid replacements Change in the amino acid sequence can alter the charges, and secondary and tertiary structure of a protein, and thus its function

Crop plants have been modified to produce their own insecticides Toxin

Genes for the toxin have been isolated, cloned, and modified, and inserted into plant cells using the Ti plasmid vector

Metagenomics

Genetic diversity is explored without isolating intact organisms

Founder effect

Genetic drift also affects small populations that colonize a new region The colonizing population is unlikely to have all the alleles present in the whole population This is founder effect- equivalent to a population bottleneck

Genetic drift and populations size

Genetic drift is more likely to occur in a small population, leading to fixation of an allele and loss of others, but less likely in a large population, where random events are buffered

Genotype

Genetic makeup of an organism is the genotype

Concerns over biotechnology

Genetic manipulation is an unnatural interference in nature Genetically altered foods are unsafe to eat Genetically altered crop plants are dangerous to the environment

What have we learned from sequencing prokaryotic genomes? Genome sequencing

Genome sequencing provides insights into microorganisms that cause human diseases and reveal new methods to combat them. Sequencing also reveals relationships between pathogenic organisms, suggesting that genes may be transferred between different strains

Genotype frequencies _____ be predicted from allele frequencies

Genotype frequencies can be predicted from allele frequencies

Generation I (founder population)

Genotype: AA (0.45) Aa(0.20) aa(0.35) Frequency of genotypes in population (not in HW equilibrium): f(AA)= 0.45 f(Aa)=0.20 f(aa)=0.35 Frequency of alleles in population (remains constant): f(AA)= 0.45+.1 p=0.55 f(aa)=0.35+.1 q=0.45

Sequence comparison

Gives a count of the minimum number of differences between two species But this underestimates the number of actual substitutions that have occurred

Some transgenic crops are resistant to herbicides

Glyphosate is widely used to kill weeds Expression vectors have been used to make plants that synthesize so much of the target enzyme of glyphosate that they are unaffected by the herbicide The gene has been inserted into corn, soybeans, and cotton A large proportion of cotton and soybean plants now carry this gene

Reporter Gene Jellyfish

Green fluorescent protein, which normally occurs in a jellyfish, emits visible light when exposed to UV light The gene for this protein has been isolated and incorporated into vectors as a reporter gene

Comparisons of eukaryotic proteomes

Has revealed a common set of about 1,300 proteins that provide the basic metabolic functions

Comparisons of prokaryote and eukaryotes genomes

Have revealed some evolutionary relationships between genes Other work is being done on primates: the chimpanzee shares 95% of the human genome and the rhesus macaque shares 91%

Why is the sickle-cell anemia allele more frequent in individuals of sub-Saharan African descent? Select one: -The disease is not as debilitating in sub-Saharan Africa, and so the allele has not been selected against in this population. -Heterozygous individuals have a fitness advantage in sub-Saharan Africa. -Because it is caused by a recessive allele, the disease is not expressed and therefore not selected against. -Heterozygous individuals generally have higher fitness than homozygous individuals, and so the allele is maintained even though it's rarely expressed. -The mutation recently arose in sub-Saharan Africa and although it is decreasing, natural selection has not had enough time to get rid of it altogether.

Heterozygous individuals have a fitness advantage in sub-Saharan Africa. This answer is correct because the allele is maintained due to the advantage in malaria resistance conferred by heterozygous individuals who do not have a fatal form of the disease, and pass on the allele.

The Human Genome Project used two approaches:

Hierarchical sequencing Shotgun sequencing

Three additional ways of manipulating DNA

Homologous recombination (knockout experiments) Prevent gene expression by complementary RNA DNA microarrays

Why would traits that make an individual more susceptible to predation and other costs be attractive to a potential mate?

Honest Advertising hypothesis Good Genes hypothesis Fisherman Arbitrary Choice hypothesis

Evolutionary change

How genetic structure of a population changes over time is a measure of evolutionary change

Anatomical homologies

Human arm and bird wing bone structure

Why do humans typically have lower gene density than bacteria? Select one: -Eukaryotes tend to have smaller, more streamlined genomes than prokaryotes. -Bacteria do not have regulatory sequences in their DNA. -Humans have many introns. -All answers are correct. -None of the answers are correct.

Humans have many introns.

Expression Vectors

Include sequences needed for expression of the transgene in the host cell

If a locus has two alleles, A and a Genotypes Polymorphic

If a locus has two alleles, A and a, there could be three genotypes: AA, Aa, and aa The population is polymorphic at that locus

Selective force

If allele percent has changed from generation to generation, a selective force has occurred

If an amino acid position is under positive selection for change...

If an amino acid position is under positive selection for change, the rate of non synonymous substitutions should be much higher than synonymous

If an amino acid position is under purifying selection...

If an amino acid position is under purifying selection, the rate of synonymous substitutions should be much higher than non synonymous

If an amino acid replacement is neutral with respect to fitness...

If an amino acid replacement is neutral with respect to fitness, the two rates would be expected to be similar; the ratio would be close to one

If certain conditions are met, the genetic structure of a population __________ change over time

If certain conditions are met, the genetic structure of a population does not change over time

Natural selection can act on characters with quantitative variation in three ways: Directional selection Evolutionary trend

If directional selection operates over many generations, an evolutionary trend occurs Long-term examples of directional selection abound in fossil record Horns of Texas Longhorn cattle have evolved through directional selection; predation was the selection pressure

Using Transposon Mutagenesis to Determine the minimal Genome Conclusion

If each gene is inactivated in turn, a 'minimal essential genome' can be determined

Population bottleneck

If populations are reduced to a small number of individuals- a population bottleneck- genetic drift can reduce the genetic variation A population forced through a bottleneck is likely to lose much genetic variation

Monomorphic

If there is only one allele at a locus, its frequency=1 The population is monomorphic at that locus; the allele is said to be fixed

Comparative genomics

In comparative genomics, newly sequenced genomes are compared with sequences from other organisms This can give information about the functions of sequences, and is used to trace evolutionary relationships

Everyday speech Theory

In everyday speech, "theory" means an untested hypothesis, or a guess

The Human Genome Project used two approaches: Hierarchical sequencing

In hierarchical sequencing, short marker sequences are identified- ensuring that every DNA fragment would have a marker

Polyploid organisms

In polyploid organisms, the whole genome is duplicated, providing opportunities for new functions to arise Example: Jawed vertebrates have four diploid sets of many major genes Two genome duplication events may have occurred in the ancestors of these species. It has allowed specialization of individual genes

Nonsynonymous substitution rates vary Protein-coding regions

In protein-coding regions, synonymous substitutions occur five times more rapidly than non synonymous substitutions The rate is even higher in pseudogenes

In science Theory

In science, "theory" refers to the entire body of work on the understanding and application of a field of knowledge

Darwin Galapagos Islands

In the Galapagos Islands Darwin observed that species were similar to, but not the same as, species on the mainland of South America. He also realized that species varied from island to island

Natural selection can act on characters with quantitative variation in three ways: Disruptive selection continued

Individuals at either extreme are more successful than average individuals Example: Bill size in black bellied seed crackers Birds with large bills can crack the hard seeds of one sedge species. Birds with small bills feed more efficiently on the soft seeds of a different sedge species

Individuals do not ________; populations do.

Individuals do not evolve; populations do

Which of the following is the mechanism that drives natural selection? Select one: -Individuals with traits better suited to their environments are more likely to survive and reproduce; therefore, their offspring are more likely to inherit these adaptive traits. -Individuals with traits better suited to their environments are more likely to survive and reproduce; however, their offspring are not likely to inherit these adaptive traits. -Individuals with traits that are not suited to their environments are more likely to leave and reproduce elsewhere; therefore, offspring will inherit these traits. -Traits that are best suited to their environments are more likely to survive and reproduce; therefore, offspring are more likely to inherit these adaptive traits -None of the answers are correct.

Individuals with traits better suited to their environments are more likely to survive and reproduce; therefore, their offspring are more likely to inherit these adaptive traits.

Expression vectors may also have:

Inducible promoters Tissue-specific promoters Signal sequences

Three types of polymorphisms: Single nucleotide polymorphisms (SNPs)

Inherited variations involving a single base- point mutations

Why was the shotgun sequencing approach a faster way of sequencing the genome than using the three-stage approach? Select one: -Instead of focusing carefully on mapping and ordering, shotgun sequencing relied on a computer program to organize sequenced DNA fragments. -It produced several genome sequences from which to choose. -It focused only on the coding regions of the genome. -It relied only on existing genomic information rather than providing new information. -It avoided the sequencing step.

Instead of focusing carefully on mapping and ordering, shotgun sequencing relied on a computer program to organize sequenced DNA fragments.

Primary metabolites

Involved in normal processes, such as in pathways like glycolysis Also includes hormones and other signaling molecules

Measuring metabolites

Involves gas chromatography and high-performance liquid chromatography, which separate molecules Mass spectrometry and nuclear magnetic resonance spectroscopy are used to identify them

Which of the following is a unique property of evolution by gene flow? Select one: -There will be a change in allele frequency after several generations. -It results in decreased variation. -Alleles that help confer an advantage to an individual in a given environment will increase in frequency. -It can result in an increase in genetic variation. -All answers are correct.

It can result in an increase in genetic variation.

Expression vectors may also have: Inducible promoters

Respond to a specific signal

Both dragonflies and pigeons have wings. What insight can this fact give us about evolution? Select one: -It suggests that dragonflies and pigeons share a common ancestor that had wings. -It demonstrates that evolution can give rise to traits that perform similar functions multiple, independent times. -It is an example of descent with modification. -It is not informative about evolution because the two species do not share a common ancestor. -They are examples of homologous structures.

It demonstrates that evolution can give rise to traits that perform similar functions multiple, independent times.

It is estimated that ____ percent of the microbial world has been invisible to biologists and is only now being revealed by __________

It is estimated that 90% of the microbial world has been invisible to biologists and is only now being revealed by metagenomics

Which characteristic makes it least likely that an organism will be preserved in a fossil? Select one: -It became extinct because a volcanic explosion covered its territory in ash. -It lived in a tropical rain forest. -It was abundant on the Eurasian continent at one time. -It has a skeleton made of bones. -It became extinct 5,000 years ago.

It lived in a tropical rain forest.

Which of the following is true of a cline? Select one: -It reflects genetic variation among populations. -It increases genetic variation by causing mutations. -It is the result of two populations that cannot interbreed. -It decreases genetic variation. -It is the result of distinct, rapidly changing environments.

It reflects genetic variation among populations.

The Haemophilus influenzae bacillus is a prokaryotic organism. From this fact, what can you conclude about the size of its genome? Select one: -Its genome is likely to be very large. -Its genome is likely to be very small. -Its genome is likely to be larger than that of most eukaryotes. -Its genome is likely to be smaller than that of most eukaryotes. -None of the answers are correct.

Its genome is likely to be smaller than that of most eukaryotes.

Evolution is constrained in many ways

Lack of genetic variation can prevent evolution of potentially favorable traits If the allele for a given trait does not exist in a population, that trait cannot evolve, even if it would be favored by natural selection

The fossil record provides direct evidence for evolutionary relationships among living organisms and the history of life. So why is it controversial? Select one: -Many fossils were likely buried by scientists themselves. -Fossil evidence suggests that the Earth is much older than what is written in religious texts. -The fossil record suggests that species have gone extinct in the past. -Large gaps in the record suggest there is not enough evidence to support descent with modification. -All answers are correct.

Large gaps in the record suggest there is not enough evidence to support descent with modification.

Species vary in the rate of gain or loss of functionless DNA Possible reasons:

Large genomes can slow the rate of development and may be selected against Amount of noncoding DNA may be related to population size. In small populations genetic drift may overwhelm selection against these sequences

Alternative splicing

Leads to different combinations of exons in the mature mRNAs Post translational modifications also increase the number of proteins that can be derived from one gene

Models

Models also extend sequence alignments across multiple homologous sequences The minimum number of changes can be summed for entire groups of organisms The revised estimate accounts for the total number of substitutions likely to have occurred between two sequences (usually more than the observed number of differences)

Conceptual Approach to Population Genetics

Let big A and a equal the alleles of a single gene that codes for some characteristic Let p= frequency of A allele Let q= frequency of a allele Suppose individuals do not choose mating partners based on this trait= random mating with respect to this trait- this is like having a crap shoot with who mates with who- could consider all alleles in environment as different colored marbles The chance of getting AA is just probability of that pick Gene pool= alleles are 'picked' at random to form the next generation Suppose Aa+ Aa - punnet square= AA, Aa, aA, aa 1AA: 2 Aa: 1 aa Probability pq X pq 'and rule' Double dominant AA p*p=p^2 Heterologous p*q Double recessive= q^2 p+q=1.0 p^2= frequency of AA 2pq= frequency of Aa q^2= frequency aa p^2+2pq+q^2=1.0 p^2+2pq+q^2=1.0 Gametes are being produced in equal frequencies

Four types of Transposons LINEs

Long interspersed elements Some are transcribed and translated into proteins

What have we learned from sequencing prokaryotic genomes? Transposons

Longer transposable elements (up to 5,000 base pairs) carry additional genes and are called transposons Sometimes these DNA regions contain a gene for antibiotic resistance

Sexual selection long-tailed widow birds

Male tails were shortened or lengthened Both were able to successfully defend their territories, but males with lengthened tails attracted more females Long tails indicate the health and vigor of the male

Difference between sexes, sexual dimorphism, depends on investment of each sex in offspring Pretty females

Males invest more in offspring Females invest more in attractiveness

Pseudogenes

Many gene families include nonfunctional pseudogenes, resulting from mutation that causes a loss of function A pseudogene may simply lack a promoter and thus fail to be transcribed; or a recognition site needed for the removal of an intron

Neutral allele

Many mutations do not affect the function of the resulting proteins An allele that does not affect fitness is a neutral allele. They tend to accumulate in a population Molecular techniques allow neutral alleles to be identified and used to study divergence of populations and species

Synonymous or silent substitution

Many nucleotide substitutions have no effect on phenotype because most amino acids are specified by more than one codon A substitution that does not change the amino acid that is specified is a synonymous or silent substitution

Sequence alignment technique To correct for underestimation

Mathematical models are developed that describe how DNA and protein sequences evolve For example, transitions (changes between two purines or two pyrimidines) are more frequent than transversions (change between a purine and a pyrimidine)

Conditions that must be met for Hardy-Weinberg equilibrium

Mating is random Population size is infinite- large populations aren't affected by genetic drift No gene flow No mutation Natural selection does not affect survival of any genotypes

Genotype frequencies

May not be the same as allele frequencies

DNA can also be analyzed directly from environmental samples

Metagenomics

gene flow

Migration into or out of the population

noncoding DNA

Much of the noncoding DNA, which is the vast majority of DNA in most eukaryotic genomes, does not appear to have a function Some noncoding DNA can alter the expression of surrounding genes Some noncoding DNA consists of pseudogenes Some consists of parasitic transposable elements

Which of the following statements about diseases with multifactorial causes is true? Select one: -Multifactorial diseases are caused by environmental factors. -Multifactorial diseases are caused by genetic factors. -Multifactorial diseases are caused by environmental and genetic factors. -Multifactorial diseases are caused by a single mutation in a gene. -Multifactorial diseases are caused by pathogens like bacteria and viruses.

Multifactorial diseases are caused by environmental and genetic factors.

Several events could have occurred at any given nucleotide

Multiple substitutions Coincident substitutions Parallel substitutions Back substitutions

Hardy-Weinberg equilibrium is a null hypothesis that assumes evolutionary forces are absent Known evolutionary mechanisms:

Mutation Gene flow Genetic drift Nonrandom mating Natural selection

Three types of polymorphisms: Restriction fragment polymorphisms (RFLPs)

Mutations in restriction sites that prevent normal enzyme cutting are restriction fragment polymorphisms (RFLPs) Can be seen as bands on an electrophoresis gel The band pattern is an inherited characteristic

Myoglobin

Myoglobin is less complex, but has a much higher affinity for O2; it stores O2 in muscle tissue A phylogenetic tree of gene sequences has been constructed for the globin gene family The rate of divergence for globin genes is about one substitution every two million years

Which of the following population sizes (N) of bison would be most affected by genetic drift? Select one: N = 10 N = 100 N = 1,000 N = 10,000 -All the populations would be equally affected.

N = 10

Natural selection phenotype

Natural selection acts on the phenotype rather than directly on the genotype

What is the relationship between natural selection and evolution? Select one: -They are the same thing. -The need for evolution causes natural selection to occur. -Natural selection changes a species in a short period of time, whereas evolution takes much longer. -Natural selection is one process that can result in evolution. -Natural selection only causes adaptations in allele frequencies, whereas evolution can adapt an entire species.

Natural selection is one process that can result in evolution.

The roundworm Caenorhabditis elegans has a gene density of about 200 genes/Mb. What would be your best estimate of the gene density of a laboratory rat, Rattus norvegicus? Select one: -No estimate can be made based on this data. -100 genes/Mb -1,000 genes/Mb -2,000 genes/Mb -200 genes/Mb

No estimate can be made based on this data.

Nonrandom mating

Occurs when individuals choose mates with particular phenotypes If individuals choose the same genotype as themselves, homozygote frequencies will increase

Secondary metabolites

Often unique to particular organisms or groups Examples: Antibiotics made by microbes, and chemicals made by plants for defense against pathogens and herbivores

Several events could have occurred at any given nucleotide Back substitutions

One change at a position is changed back to the original (reversions)

Using Transposon Mutagenesis to Determine the minimal Genome Hypothesis

Only some of the genes in a bacterial genome are essential for cell survival

What is the difference between the honest-advertising and good-genes mechanisms of sexual selection? Select one: -A phenotype that increases mating success is passed on in the good-genes mechanism, while "honest advertising" signals a phenotype that increases fitness of the mate. -Only the good-genes mechanism signals an advantage of a specific trait. -"Good" genes increase mating success but do not necessarily have any other advantage, while honest-advertising genes indicate that an individual is healthy. -Honest advertising is an example of intersexual selection and the good-genes mechanism is an example of intrasexual selection. -Good genes result in sexual dimorphism but honest advertising does not.

Only the good-genes mechanism signals an advantage of a specific trait. This answer is correct because in the good-genes mechanism, preferred phenotypes of mates are those that signal the presence of a specific heritable advantage, whereas in the honest-advertising mechanism, the preferred phenotype is a general indicator of good health.

Genome sequence information is used to identify:

Open reading frames or coding regions Amino acid sequences of proteins Regulatory sequences RNA genes Other noncoding sequences

What statement concerning genome size and organism characteristics is correct? Select one: -The larger the organism, the larger the genome size. -Prokaryotes have larger genome sizes than eukaryotes. -Genome size does not relate to the functional complexity of an organism at all. -Organisms that carry out simpler functions may have larger genome sizes than more complex organisms. -None of the answers are correct.

Organisms that carry out simpler functions may have larger genome sizes than more complex organisms.

Palindromic DNA Sequences

Restriction enzymes recognize palindromic DNA sequences: 5'... GAATTC...3' 3'... CTTAAG...5' Some make straight cuts, others make staggered cuts, resulting in overhangs or sticky ends

Genetic variation

Populations have genetic variation for many characteristics For example, artificial selection for different characters in a single species of wild mustard produced many crop plants This was possible because the original mustard population had genetic variation for the characters of interest

Populations in nature

Populations in nature rarely fit the conditions for Hardy-Weinberg equilibrium However, it is useful for predicting genotype frequencies from allele frequencies Also, because the model describes conditions that would result in no evolution, patterns of deviation from the model help identify mechanisms of evolution

Natural selection can act on characters with quantitative variation in three ways: Stabilizing selection

Preserves average phenotype on graph: phenotype in the middle have the highest fitness, those individuals produce more offspring resulting in selection occurring and eliminating extremes and more individuals are in the mean Occurs in stable environments

Some Medically Useful Products of Biotechnology Vaccine proteins: Hepatitis B, Herpes, Influenze, Lyme disease, meningitis, pertussis ect

Prevent and treat infectious diseases

Some Medically Useful Products of Biotechnology Erythropoietin

Prevents anemia in patients undergoing kidney dialysis and cancer therapy

Pharming

Production of pharmaceuticals in farm animals or plants Example: Transgenes are inserted next to the promoter for lactoglobulin- a protein in milk. The transgenic animal then produces large quantities of the protein in its milk

Genetic drift

Results from random changes in allele frequencies Harmful alleles may increase in frequency, and rare advantageous alleles may be lost In large populations, genetic drift can influence frequencies of alleles that don't affect survival and reproduction

Some interesting facts about the human genome:

Protein-coding regions make up less than 2 percent, about 24,000 genes Each gene must code for several proteins, and post transcriptional mechanisms (e.g. alternative splicing) must account for the observed number of proteins in humans An average gene has 27,000 base pairs All human genes have many introns Over 50% of the genome is transposons and other repetitive sequences 97% of the genome is the same in all people Genes are not evenly distributed over the genome. The Y chromosome has the fewest (231); chromosome 1 has the most (2,968)

Proteins have different functional regions or domains

Proteins that are unique to a particular organism are often just unique combinations of domains that exist in other organisms

The fossil record

Provides a physical history of how life has evolved over billions of years Can help determine relationships between modern and ancient groups

Which of these mRNA sequences could be produced by the alternative splicing of a DNA segment with the exon sequence Q R S T? Select one: Q Q S T Q S T Q S R T T S R Q All the sequences in the other choices can be produced by alternative splicing.

Q S T

Which technique can be used to knock down gene expression? Select one: -gel electrophoresis -in situ hybridization -microarray -genome-wide association study -RNA interference

RNA interference

RT-PCR and in situ hybridization are both methods used to detect expression of a single gene. How do the circumstances of their use differ? Select one: -The question is not correctly worded. RT-PCR is a way to analyze expression of a single gene, but in situ hybridization must involve several genes at once. -RT-PCR serves to amplify the gene so that its expression may be confirmed, while in situ hybridization provides a strictly quantitative measure of expression. -RT-PCR is a method of quantifying gene expression, while in situ hybridization is largely useful for localizing where a gene is expressed. -RT-PCR is a method of sifting out which tissues express a gene by running all the tissues at once, while in situ hybridization may only provide information about a single tissue at a time. -RT-PCR involves cutting the gene into pieces and quantifying those pieces for expression information, while in situ hybridization involves examination of the expression of the whole gene at once.

RT-PCR is a method of quantifying gene expression, while in situ hybridization is largely useful for localizing where a gene is expressed.

C-14

Radiometric dating methods, like C-14 dating, inform us about the ages of fossils and other materials

Genetic drift

Random fluctuation in allele frequency

Transformation

Recombinant DNA is cloned by inserting it into host cells (transfection if host cells are from an animal)

Recombinant DNA technology can be used to ______

Recombinant DNA technology can be used to clone, or make identical copies of genes

Natural selection can act on characters with quantitative variation in three ways: Stabilizing selection purifying selection

Reduces variation in a population, but does not change the mean Rate of evolution are slow because natural selection is usually stabilizing For specific genes, stabilizing selection is often called purifying selection, because there is selection against deleterious mutations

How can different evolutionary processes be distinguished?

Relative rates of synonymous and non synonymous substitutions should vary in genes undergoing different types of selection

Eukaryotic genomes have repetitive DNA sequences: Moderately repetitive sequences

Repeated 10-1,000 times Includes the genes for tRNAs and rRNAs Single copies of the tRNA and rRNA genes would be inadequate to supply the large amounts of these molecules needed by cells

Some Medically Useful Products of Biotechnology Factor VIII

Replaces clotting factor missing in patients with hemophilia A

Some Medically Useful Products of Biotechnology Growth Hormone

Replaces missing hormone in people of short stature

Crops with improved nutritional characteristics

Rice does not have B-carotene, but does have a precursor molecule Genes for enzymes that synthesize B-carotene from the precursor are taken from daffodils and inserted into rice by the Ti plasmid The transgenic rice is yellow, and can supply B-carotene to improve the diets of many people B-carotene is converted to vitamin A in the body

Four types of Transposons

SINEs LINEs Retrotransposons DNA transposons

Yeast

Saccharomyces Cerevisiae

Several events could have occurred at any given nucleotide Parallel substitutions

Same substitution in different descendants

Reporter Gene

Selectable markers are a type of reporter gene- a gene whose expression is easily observed by the phenotype of the cells that carry them Many plasmids contain the lacZ gene with a multiple cloning site within its sequence. LacZ codes for an enzyme that can convert the substrate X-Gal into a bright blue product

Model organisms

Several model organisms have been studied extensively Model organisms are easy to grow and study in a laboratory, their genetics are well studied, and they exhibit characteristics that represent a larger group of organisms

Homologies

Shared similarities between species inherited from a common ancestor Sometimes homologies are observable only during development, as in many vertebrate embryos

Four types of Transposons SINEs

Short interspersed elements are transcribed but not translated

Three types of polymorphisms: Short tandem repeats (STRs)

Short repetitive sequences occurring side by side on chromosomes, usually in noncoding regions. Also known as VNTRs (variable number tandem repeats)

Eukaryotic genomes have repetitive DNA sequences: Highly repetitive sequences

Short sequences (<100 base pairs) repeated thousands of times in tandem; not transcribed Short tandem repeats (STRs) of 1-5 base pairs can be used in DNA fingerprinting

Three types of polymorphisms:

Single nucleotide polymorphisms (SNPs) Short tandem repeats (STRs) Restriction Fragment Polymorphisms (RFLPs)

Plasmids make good vectors:

Small and easy to manipulate Have one or more restriction enzyme recognition sequences that each occur only once Many have genes from antibiotic resistance which can be selectable Have a bacterial origin of replication (ori) and can replicate independently of the host chromosome

Plant metabolomics has been studied for many years

Tens of thousands of secondary metabolites have been identified The metabolome of the model organism Arabidopsis thaliana is now being described

As the proteome changes

So will the abundances of metabolites

Results

Some E. Colie are resistant to both antibiotics

Observations on natural selection:

Some heritable traits are favored over others

These observations, and many others, led Darwin to propose an explanatory theory for evolutionary change based on three propositions:

Species change over time Divergent species share a common ancestor The mechanism that produces the change is natural selection Offspring resemble parents because some traits are heritable Individuals produce far more offspring than can survive, therefore offspring compete for resources Some traits confer an advantage to individuals possessing them, thus increasing their chances to produce offspring themselves; those traits therefore increase in frequency

Recombinant DNA technology has several advantages

Specific genes can be targeted Any gene can be introduced into any other organism New organisms can be generated quickly

Natural selection can act on characters with quantitative variation in three ways:

Stabilizing selection Directional selection Disruptive selection

Some Medically Useful Products of Biotechnology Insulin

Stimulates glucose uptake from blood in people with insulin-dependent (Type I) diabetes

Some Medically Useful Products of Biotechnology Colony-stimulating factor

Stimulates production of white blood cells in patients with cancer and AIDS

Some Medically Useful Products of Biotechnology Platelet-derived growth factor

Stimulates wound healing

The field of molecular evolution

Study of the mechanisms and consequences of the evolution of macromolecules The relationships between the structure of genes and proteins and organism function Using molecular variation to reconstruct evolutionary history

Gene families

Successive rounds of duplication and mutation can result in gene families, such as the globin gene family Amino acid sequencing of globins suggests they arose via gene duplications Hemoglobin is a tetramer of two alpha globin and two beta globin chains that carries O2, CO2, and H+

Some genes are unique to plants

Such as those involved in photosynthesis, water transport, assembly of the cell wall, and making molecule for defense against microbes and herbivores

Conceptualizing Natural Selection

Suppose a population with differential phenotypes Orange individuals, blue individuals, red individuals - will be aspects of these phenotypes that are heritable (some may be due to environment) -Variation arising by mutations - Suppose environment can support 10 total offspring from these three individuals, but these critters are going to produce more than that number of offspring Orange=4 offspring blue=5 offspring Red= 4 offspring Offspring= more produced than can survive= offspring are going to be competing against each other in competition for limited resources Some individuals are going to be able to compete better than others because of their phenotype If 2 orange die and 1 red dies Competition and failure to reproduce leaves us with 2 orange, 5 blue, 3 red If all individuals reproduce and reproduce the same amount as their parents did would have: offspring produced: 8 offspring from 2 orange from 3 red; 25 offspring from 5 blue -Because of differential phenotype success, and from generation to generation, blue and red are more selectable than orange -if a trait confers a reproductive advantage, it will increase in frequency from one generation to the next -For given phenotypes in given environment (if environment changes, favored phenotype could change)

Advocates of biotechnology point out:

That all crop plants have been manipulated by humans Since only single genes for plant function are inserted into crop plants, they are still safe for human consumption Genes that affect human nutrition may raise more concern

How does the Church of England's initial response to Darwin's ideas compare with their current position? Select one: -The Church was hostile to Darwin's work for many years but now accepts a scientific explanation of evolution. -In Darwin's time, the Church rejected all science. It now accepts science, but not evolution. -The Church originally supported his work but now rejects it. -The Church's position on evolution has not changed. -The Church initially did not take a position on evolution but now accepts it.

The Church was hostile to Darwin's work for many years but now accepts a scientific explanation of evolution.

The Human Genome Project used two approaches: Hierarchical sequencing continued

The DNA from each clone is then cut and sequenced Overlapping parts of the sequences are aligned (with the aid of computers) to create the complete sequence of the BAC clone Then the larger fragments are arranged in proper sequence along the chromosome map

Which of the following statements is TRUE regarding the effect of a single mutation in one individual on evolution? Select one: -The allele can increase in frequency drastically, but it would take a very long time to detect. -It would have a small effect; evolution usually requires changes in many genes to be detected. -The allele can increase in frequency drastically and rapidly. -The mutation would have no effect. Individual mutations are usually lethal and are therefore not passed on. -It would be difficult to measure because detection of evolution requires many individuals with the same mutation so that its frequency can be measured.

The allele can increase in frequency drastically and rapidly.

Transgenic

The altered host cell

Crop plants have been modified to produce their own insecticides Bacillus Thuringiensis

The bacterium Bacillus thuringiensis produces a protein that kills insect larvae

The _____________ of the eukaryotic yeast cell requires it to have many more genes

The compartmentalization of the eukaryotic yeast cell requires it to have many more genes

The complexity of the biological world

The complexity of the biological world makes it impossible to predict all potential environmental effects of transgenic organisms In fact, some spreading of transgenes has been detected

What have we learned from sequencing prokaryotic genomes?

The first life forms to be sequenced were the simplest viruses with relatively small genomes The first complete genomic sequence of a free-living cellular organism was for the bacterium Haemophilu influenza, in 1995

Gene pool

The gene pool is the sum of all copies of all alleles at all loci in a population The gene pool is the source of genetic variation that produces the phenotypic traits on which natural selection acts

Thale cress

The genomes of some plants are huge, but A. thaliana has a much smaller genome Many of the genes found in animals have homologs in plants, suggesting a common ancestor

Neutral theory of molecular evolution

The majority of mutations are neutral, and accumulate through genetic drift If most mutations are neutral, and the mutation rate is constant, macromolecules evolving in different populations should diverge from one another at a constant rate: The "molecular clock"

The new DNA must also _______ as the host cell divides

The new DNA must also replicate as the host cell divides

Replicon

The new DNA must become part of a segment with an origin of replication- a replicon or replication unit (integrates with host genome)

What did the results of the frog cloning experiments of John Gurdon and his fellow researchers show? Select one: -Animals and plants respond to cloning in basically the same way. -The age of the cell providing the nucleus does not matter. -The nucleus of a differentiated animal cell does not contain instructions to direct the development of an organism. -All frog cells are totipotent. -The nucleus of a differentiated cell contains the instructions to direct the development of an organism.

The nucleus of a differentiated cell contains the instructions to direct the development of an organism.

DNA fragments separate and give three types of information:

The number of fragments The sizes of the fragments The Relative abundance of the fragments, indicated by the intensity of the band

Mutation

The origin of genetic variation Most (not all) mutations are harmful or neutral A few are beneficial; or if conditions change, a mutation could become advantageous Mutations can also restore genetic variation that other processes have removed

Phenotype

The phenotype is the physical expression of an organism's genes

Why do scientists try to use the same restriction enzyme to excise the target DNA sequence and to cut the plasmid? Select one: -The bacteria will recognize the target DNA sequence and correctly insert it into the plasmid. -Both eukaryotes and prokaryotes can recognize the enzyme. -The DNA will be cut in both the target chromosome and in the plasmid. -Using one enzyme in a eukaryote and another enzyme in a prokaryote will result in the inability of the DNA from each organism to interact. -The plasmid and the insert will have compatible sticky ends.

The plasmid and the insert will have compatible sticky ends. This answer choice is correct because using the same restriction enzyme results in each DNA component (plasmid and target sequence) having compatible sticky ends and enhances the probability that they will stick to each other.

Expression vectors For eukaryotes

The poly A- addition sequence, transcription factor binding sites, and enhancers, must be included

A population of birds exhibits high diversity in alleles for feather color. Human settlers overhunt the population, causing a bottleneck effect. What might you predict about the population of birds that will exist after the bottleneck event? Select one: -The population will be prone to mutation because its members will begin inbreeding. -The population will experience gene flow because the birds will begin breeding with members of other populations. -The population will be more fit than before the bottleneck event because only the fittest individuals will have survived and reproduced. -The population will have less diversity in feather color because the variety of alleles will be reduced. -None of the answers are correct.

The population will have less diversity in feather color because the variety of alleles will be reduced.

Adaptation

The processes by which useful characteristics evolve; also refers to the characteristics themselves

Allele frequency

The proportion of an allele in a population

When a scientist analyzes gene function using gene knockout techniques, what is the ultimate outcome? Select one: -The protein that the gene encodes is not made. -The gene expresses a protein, but the protein only functions at half activity. -The mRNA is translated but not transcribed. -Gene expression will double to make up for the changes. -The gene exhibits a new function, which allows the scientists to determine what else it may do.

The protein that the gene encodes is not made.

Metabolome

The quantitative description of all of the small molecules in a cell or organism

Fitness of a phenotype is determined by

The relative rates of survival and reproduction of individuals with that phenotype

Fitness

The reproductive contribution of a phenotype to subsequent generations relative to other phenotypes is called its fitness

The Human Genome Project used two approaches: Shotgun sequencing

The shotgun sequencing method cuts DNA into smaller, overlapping fragments that are cloned and sequenced at the ends Computers are used to search for overlapping markers This approach is much faster and cheaper

Trait

The specific form of a character is a trait (e.g. blue)

Proteome

The sum total of proteins produced by an organism; it is more complex than the genome The aim of proteomics is to identify and characterize all of the expressed proteins

What does the term gene ontology refer to? Select one: -The term refers to breaking a gene sequence into its component parts. -The term refers to genes that are active in the embryo. -The term refers to the standardized vocabulary researchers use to annotate genes in databases. -The term refers to the linkage mapping used in the shotgun sequencing approach. -The term refers to the development of a gene sequence.

The term refers to the standardized vocabulary researchers use to annotate genes in databases.

Evolutionary Theory

The understanding and application of the mechanisms of evolutionary change to biological problems

Biotechnology

The use of living cells or organisms to produce materials useful to people Examples: Using yeasts to brew beer and wine Using bacteria to make cheese, yogurt etc. Using microbes to produce antibiotics, alcohol, and other products

Charles Darwin

The young Charles Darwin was passionately interested in geology and natural science In 1831 he was recommended for a position on the H.M.S. Beagle, for a five-year survey voyage around the world

What have we learned from sequencing prokaryotic genomes? Transposable Elements

Transposable elements are DNA sequences that can move from place to place in the genome or to a plasmid If a transposable element is inserted into the middle of a gene, it will be transcribed, and result in abnormal proteins

A labradoodle is a dog created from the mating of a Labrador retriever, known for its gentle nature, and a poodle, known for its low-shed coat. How does breeding of domesticated animals contrast with natural selection? Select one: -Breeding prevents the animals from passing favorable characteristics to the next generation. -Artificial breeding will eliminate the Labrador and poodle populations, and natural selection will increase their populations. -Breeding is more effective at selecting for adaptive traits for survival than natural selection is. -They are similar except that in natural selection the traits selected increase a population's fitness, while in artificial selection humans select for a trait that they desire, which may or may not improve the organism's fitness. -Natural selection and breeding are the same.

They are similar except that in natural selection the traits selected increase a population's fitness, while in artificial selection humans select for a trait that they desire, which may or may not improve the organism's fitness

Key to evolution

This reshuffling of the genetic deck is a key to evolution

Threatened and endangered species

Threatened and endangered species can lose genetic diversity due to drift, impeding their potential recovery ex. bearded vulture conservation in Europe

Humans have been altering the traits of plants and animals

Through cultivation and selective breeding, humans have been altering the traits of plants and animals for thousands of years

Three types of polymorphisms: Restriction fragment polymorphisms (RFLPs) Analyzing RFLPs

To analyze RFLPs, DNA fragments are transferred onto a nylon membrane, then denatured to separate double strands A labeled probe- a single strand containing part of the RFLP sequence is added It hybridizes with the DNA band containing the RFLP. The label allows identification

Sequencing Genomes

To sequence an entire genome, the DNA is first cut into fragments about 500 base pairs long The haploid human genome has about 3.3 billion base pairs, resulting in 6 million fragments The fragment sequences are put together using larger, overlapping fragments

What have we learned from sequencing prokaryotic genomes? Microorganisms

Traditionally, microorganisms have been identified by culturing them in the laboratory Now, PCR and DNA analysis allow microbes to be studied without culturing

Why would traits that make an individual more susceptible to predation and other costs be attractive to a potential mate? Honest Advertising hypothesis

Traits indicate a mate that has energy to spare, indicating overall good health

Why would traits that make an individual more susceptible to predation and other costs be attractive to a potential mate? Good Genes hypothesis

Traits signal the presence of a beneficial gene

Crop plants have been modified to produce their own insecticides Reduced Pesticide

Transgenic corn, cotton, soybeans, tomatoes, and other crops are bing grown. Pesticide use is reduced

Conclusion

Two DNA fragments with different genes can be joined to make a recombinant DNA molecule, and the resulting DNA is functional

Two techniques are used to analyze the proteome

Two-dimensional gel electrophoresis separates proteins based on size and electric charge Mass spectrometry identifies proteins by their atomic masses

Selectable Marker

Usually only a few cells are transformed To determine which of the host cells contain the new sequence, the recombinant DNA includes selectable marker genes, such as genes that confer resistance to antibiotics

Host Cells Vector

Usually only a small proportion of host cells take up the vector (1 cell in 10,000) and they may not have the appropriate sequence Host cells with the desired sequence must be identifiable Selectable markers such as antibiotic resistance genes can be used

Evolution of influenza viruses

We can directly observe the evolution of influenza viruses, but it is evolutionary theory that allows us to apply that information to the development of vaccines

When genes from one kind of organism are inserted into a different organism

When genes from one kind of organism are inserted into a different organism, a promoter and other regulatory sequences from the host organism are also required

In screening for bacterial colonies containing recombinant plasmids, which color indicates that the recombinant plasmid is present? Select one: pink green blue brown white

White This answer choice is correct because the usual color choices in a screening are blue and white, and white indicates the presence of a recombinant plasmid. White indicates that the lacZ gene was interrupted by insertion of the gene of interest.

Would identical twins be expected to have very similar patterns of short tandem repeats (STRs)? Why or why not? Select one: -No. They will have different patterns because their genomes are identical only in their coding sequences, not in the non-coding parts. -Yes. Because barring any recombination after conception, their repeats will reflect their identical inheritance from the first zygotic division. -No. Their patterns would differ just as much as any other individual's because every individual is distinctly unique in their STR patterns. -Yes. Because they look alike, their patterns under a microscope will look the same too. -Yes. They will have identical patterns because STR analysis focuses only on the heritable parts of the genome that would be identical between them.

Yes. Because barring any recombination after conception, their repeats will reflect their identical inheritance from the first zygotic division.

Higher genetic variation can be advantageous in which of the following environments? Select one: -a stable environment -all environments -a mild environment -a changing environment -an extremely harsh environment

a changing environment

Genetic drift can lead to populations with reduced genetic variation. What is one evolutionary consequence of reduced genetic variation? Select one: -a decrease in stabilizing selection -a decrease in sexual selection -a decrease in environmental habitat -a decrease in the potential for adaptation to changing environments -a decrease in bottlenecks

a decrease in the potential for adaptation to changing environments

Which of the following is an example of a totipotent cell? Select one: -a hematopoietic stem cell -an inner cell mass cell -an embryonic stem cell -an induced pluripotent stem cell -a fertilized egg

a fertilized egg

In the process of using bacteria for gene cloning, what is the target DNA sequence inserted into? Select one: a probe a restriction fragment a chromosome an agar culture a plasmid

a plasmid

Enzyme activities

affect concentrations of their substrates and products, called metabolites

An alternative form of a gene that occurs in the same place on a homologous chromosome (i.e., chromosome pairs of approximately the same length with the same characteristics but each is inherited from a different parent) is ___. Select one: -homozygous -a locus -heterozygous -usually at a low frequency in the population -an allele

an allele

Yeasts and E. coli

appear to use about the same number of genes to perform basic functions

What was Darwin's interest in joining the mission of the HMS Beagle? Select one: -providing medical care for the captain and crew -assisting local people living in earthquake-prone regions -ship surgeon -providing humanitarian aid to earthquake victims in Chile -as a companion to the captain of the ship assisting in surveying the geology and biology of sites, primarily in South America

as a companion to the captain of the ship assisting in surveying the geology and biology of sites, primarily in South America

Adaptations arise

because of selective advantage

cDNA libraries

cDNA libraries are used to compare gene expression in different tissues at different stages of development

What is the name of the undifferentiated mass of tissue containing embryonic-like cells in plants? Select one: callus embryonic stem cell histone inner cell mass somatic cell

callus

Transversions

change between a purine and a pyrimidine

An endangered falcon population has been closely monitored and cared for in a protected area. Which data would be most appropriate to collect in order to best determine its recovery? Select one: -comparisons of the number of offspring produced per individual between the protected population and other healthy populations -comparison between the protected population and healthy populations of average heterozygosity in a non-coding gene sequence -comparison between the protected population and healthy populations of average heterozygosity in a sequence involved in protein synthesis -comparison of the average body size in the population before and after the protected zone was established -All answers are correct.

comparison between the protected population and healthy populations of average heterozygosity in a non-coding gene sequence

Complete the following sentence: The evolution of MRSA is NOT due to ... Select one: natural selection. selective pressure. a spontaneous mutation. overuse of antibiotics. directed mutagenesis.

directed mutagenesis.

Expression vectors may also have: Signal sequences

e.g., a signal to secrete the product to the extracellular medium

Which of the following is NOT a required component for PCR? Select one: -template DNA -primers -green fluorescent protein (GFP) -nucleotides -Taq polymerase

green fluorescent protein (GFP)

Fruit fly

has ten times more cells and is more complex than C. elegans It has a larger genome but fewer coding genes than C. elegans

Natural selection acts on which of the following? Select one: -non-heritable traits and genotypes -heritable and non-heritable traits -heritable traits and genotypes -heritable traits and phenotypes -non-heritable traits and phenotypes

heritable traits and phenotypes

In constructing an expression vector, what characteristic of the promoter is important? Select one: -infrequent use in the bacteria -Any kind of promoter is effective because the bacteria will recognize the foreign DNA sequence and activate any promoter equally. -a short promoter sequence -a long promoter sequence -highly active in the bacteria

highly active in the bacteria

What influenced Darwin's ideas about the evolution of species during his journey on the surveying mission of the HMS Beagle? Select one: -his years of training as a naturalist prior to boarding the Beagle -his observations that the finches of the Galápagos Islands all shared a unique beak shape -on-board studies of comparative anatomy and physiology -conversations with his traveling companion Alfred Russel Wallace -his experience following a major earthquake in Chile

his experience following a major earthquake in Chile

The Human Genome Project used two approaches: Hierarchical sequencing Bacterial artificial chromosomes (BAC)

in the Hierarchical sequencing approach, large DNA fragments are inserted into bacterial plasmids to create bacterial artificial chromosomes (BAC), which are then inserted into bacteria

In his original work on natural selection, Darwin was unable to provide a mechanism to explain which of the following? Select one: -selective pressures in the environment -overproduction of offspring -inheritance of traits -founder effects -competition for resources

inheritance of traits

Female widowbirds prefer males with very long tails. What is this trait an example of? Select one: -positive frequency-dependent selection -co-evolution -intersexual selection -intrasexual selection -negative frequency-dependent selection

intersexual selection

Males of Dynastes granti (a beetle) use elongated horns to compete with other males for females. They evolve long horns as a result of which process? Select one: -co-evolution -intersexual selection -frequency-dependent selection -gene flow -intrasexual selection

intrasexual selection

Complete the following sentence: The largest single component of human DNA consists of... Select one: -exons. -introns. -long interspersed nuclear sequences (LINEs). -short interspersed nuclear sequences (SINEs). -None of the answers are correct.

introns.

Gene flow

is a result of the migration of individuals and movements of gametes between populations New individuals can add alleles to the gene pool, or change allele frequencies

Artificial synthesis of DNA

is now fully automated

Tissue Plasminogen Activator: From Protein to Gene to Drug

mRNA for TPA-> Reverse transcription-> cDNA for TPA -> BamHI in Expression vector for E. coli -> Insert TPA gene-> E. Coli cell contains DNA and the genes to produce TPA-> cells produce TPA-> extract TPA and use medically

mRNA's in the cytoplasm

mRNAs don't last long in the cytoplasm and are often present in small amounts, so a cDNA library is a 'snapshot' of the transcription pattern of the cell

Pharmacogenomics

makes it possible to predict whether drug will be effective. The aim is to personalize drug treatments

The Human Genome Project used two approaches: Hierarchical sequencing Markers

markers can be short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), or recognition sites for restriction enzymes (RFLPs), among others

Imagine that you are hiking up a mountain and you notice that the trees are gradually becoming larger as you walk. You hypothesize that large size is an adaptation to colder habitats. Which of the following would NOT be informative in supporting or rejecting this hypothesis? Select one: -planting small trees in cold conditions and large trees in warm conditions and measuring their survival and their offspring's size -breeding the trees together experimentally to establish that tree size is a heritable trait -measuring variation in the sizes of trees of the same species along several other mountains in the area -measuring as many trees as possible along the mountain and plotting a graph of the relationship between temperature and tree size -None of the other answers are correct because each one describes a test that would be informative.

measuring as many trees as possible along the mountain and plotting a graph of the relationship between temperature and tree size

Many genes encode

more than one protein

For generation 1, probability of two A allele coming together is:

p*p=p^2= 0.55^2=0.3025

For generation 1, there are two ways of producing a heterozygote:

p*q or q*p or 2pq

If p is the frequency of allele A, and q is the frequency of allele a,

p+q=1 q= 1-p

allele frequency p=

p= number of copies of the allele in the population divided by the sum of alleles in the population

Hardy-Weinberg equation

p^2+2pq+q^2=1

For generation 1, probability of two a allele coming together is:

q*q=q^2=0.45^2=0.2025

What type of reproductive behavior is required to maintain Hardy-Weinberg equilibrium? Select one: -random mating -assortative/non-random mating -non-random mating -selective breeding -cross-generational

random mating

Complete the following sentence: Frequency-dependent selection is negative when ... Select one: -it reduces the size of the population. -it occurs in small populations. -it reduces the frequency of the most common phenotype. -rare phenotypes have a fitness advantage. -rare phenotypes become common.

rare phenotypes have a fitness advantage. This answer is correct because in negative frequency-dependent selection, the advantage of a phenotype increases as it becomes more rare in the population, and rare phenotypes are therefore maintained at low frequency by selection.

Refer to the above table and compare the data for humans, chicken, mice, rice, and fruit flies. Which of these organisms has the highest gene density? Select one: humans chickens mice rice fruit flies

rice

Which of the following is a genetic marker that could be linked to a disease through a genome-wide association study? Select one: -Ti -viral vectors -ATP -RNAs -single nucleotide polymorphisms (SNPs)

single nucleotide polymorphisms (SNPs)

Yeasts are

single-celled eukaryotes

Gene and protein function are both affected by

the internal and external environments of the cell

Which of the following should NOT be used as a measure of genetic diversity? Select one: -the number of methylated sequences -protein sequences -microsatellite sequences -MHC sequences -color variation in monkeyflowers

the number of methylated sequences

A new development in individualized medicine is the study of an individual's exome. These studies have revealed a strong genetic basis for some rare diseases. What is the exome? Select one: -the parts of the genome that are excised during transcription -the parts of the genome that are considered to be extra or excess -the parts of the genome that are found on the X chromosome -the parts of the genome that can exit the nucleus -the sequence of all of the coding regions of a genome

the sequence of all of the coding regions of a genome

Imagine two human populations that differ in the frequency of a specific cancer gene but are otherwise genetically similar. Which of the following metrics would be the most accurate way to determine the influence of this gene on relative fitness? Select one: -total population size -average age at first reproduction -total number of children who become reproductive themselves -All of these metrics would be informative, particularly if combined. -None of the answers are correct; genotype frequency data are needed to calculate fitness.

total number of children who become reproductive themselves

When does a hypothesis become a theory? Select one: -when the results of an experiment confirm the predictions of the hypothesis -when several experts state strong support for the proposed theory -when five different observations support the hypothesis -when several lines of evidence and multiple observations arrive at the same conclusion -There is no difference between a hypothesis and a theory.

when several lines of evidence and multiple observations arrive at the same conclusion

When calculating allele frequencies, what does the chi-square statistic tell us? Select one: -relative fitness of different alleles in a population -difference in mean fitness between two populations -whether the gene frequencies in a population differ from random expectations and change through time -Pearson's test -All answers are correct.

whether the gene frequencies in a population differ from random expectations and change through time