Unit 4

What is the purpose of using dideoxynucleotides in DNA sequencing?

Nucleotides are added at the 3' hydroxyl group (-OH) of the growing chain during DNA synthesis.

ddNTPs lack a free hydroxyl (-OH) group at the 3' carbon, thus preventing additional nucleotides from being added to the chain when a ddNTP is incorporated.

What three techniques are common to all types of sequencing

1. Chain-terminating nucleotides

2. Electrophoresis

3. Polymerase chain reaction

Shotgun sequencing

The map is:

Constitutive heterochromatin, localized near centromeres and telomeres

Structural DNA

Stuttering repeats of a few nucleotides such as CGG, repeated thousands of times

Simple sequence repeats (SSRs)

Sequence that has characteristics of a gene, but is not a functional gene

Pseudogenes

genetic maps

maps that provide relative locations of genes based on recombination frequencies

physical maps

maps that provide the actual locations of genetic landmarks

Genetic map

Map A is _______

Physical map

Map B is ______

DNA sequences that can move within a genome; sometimes referred to as "jumping genes"

Transposable Elements

The coding region of DNA in between a start codon and a stop codon is called a(n) __________.

Open reading frame (ORF)

The study of proteome or collection of proteins encoded in the genome

proteomics

Uses biotechnology to highlight the connection between the genotype and phenotype

functional genomics

Uses information from one genome to learn about a second genome

comparative genomics

Uses computer programming, mathematics, and modeling to analyze data

bioinformatics

When scientists work with DNA microarrays, what are they interpreting?

The patterns of gene (or protein) expression in a sample

Functional elements

Because there appears to be so much non-coding DNA in the human genome, the ENCODE project was created to identify ___________

80%

The ENCODE findings suggest that _______ of the human genome is functional.

"Biological activity"

The ENCODE definition of functional is any portion of the DNA that has ________

sites of DNase activity don't imply functionality

Examples of this are sites of DNA methylation, chromatin modification, and parts of the DNA that can be cut with DNase enzymes. Many critics of the ENCODE project believe that "biological activity" is not sufficient criteria to identify DNA as functional. Additional critiques are that ____________ and strongly held beliefs of evolutionary biologists.

The form of the anatomical structures is formed

Morphogenesis

The process in which a zygote undergoes to produce a new organism

Cell division

Changes in gene expression that result in cell specialization

Cell differentiation

Cells' ability to detect positional information in the body plan

Pattern formation

G2 & G1

During early development, cells undergo rapid divisions. The figure below shows the adult cell cycle. Which stages are shortened in order to allow for rapid cell division during early development? Select ALL that apply.

African Clawed Frogs (Xenopus laevis) represent a good model system for research on ___________________.

Morphogenesis

T/F: Cell differentiation is a gradual process that occurs over multiple cell divisions, thus gradually altering gene expression. It is not like turning a light switch on and off.

true

Can give rise to limited number of cell types

Multipotent stem cells

Can give rise to all the cells in an organism, but not to extraembryonic tissues

Pluripotent stem cells

Can give rise to all the cells in an organism, including extraembryonic tissues

Totipotent stem cells

Can give rise to only a single cell type

Unipotent stem cells

T/F: Hox gene complexes are highly conserved, and they play important roles during early embryonic development. These genes are responsible for determining the general body plan of an organism.

True or False: A mutation in the Hox gene complex of the fruit fly (Drosophila melanogaster) could result in an extra pair of wings / appendages / etc. growing from the "wrong" body part.

true

Necrosis

triggered by: injury

mode of action: swelling and bursting, releasing the cell's content into the extracellular fluid

Apoptosis

Triggered by: Expression of genes in the "cell death pathway"

Mode of action: Gradual degradation of cells, recycling cellular contents or digesting them

- apoptosis
- cell growth
- changes in cell shape
- cell migration
- cell division

Which of the following mechanisms are used to achieve morphogenesis?

T/F: The process of development results in irreversible changes to the DNA sequence as cells progress from a single zygote to a multicellular organism.

false

Reproductive cloning

In Method A, genetically identical copies are created; for example, an animal is created to be genetically identical to another animal. This type of cloning can be useful for reintroducing extinct species and for reproducing lines of livestock or other organisms. Method A is an example of

Therapeutic cloning

In Method B, genetically identical tissues are injected or transplanted into the patient. This type of cloning can be useful for treating autoimmune diseases and for providing rejection-free tissues to patients since the cells come from the same patient. Method B is an example of

T/F: An organism's phenotype - its apparent physical characteristics - is influenced by both its genotype and by the environment.

true

Evolution is defined as changes in allelic frequencies in ________ over time

populations

This means that ___________ do NOT evolve.

Individuals

Which of the following mechanisms of evolution is considered to be the ultimate source of genetic variation?

Mutation

Pesticide resistance has been observed in many different species of pests. Why would pesticide resistance likely evolve in a species?

Several individuals have a genetic mutation that confers resistance to the pesticide, and these pests do not die when the pesticide is applied.

Gene flow

The image above shows the movement of a red bird from its normal habitat to one that consists of blue birds. Likewise, a blue bird moves from its normal habitat to one that consists of red birds. This is an example of gene flow , which can be a powerful agent of change.

- no mutation takes place
- no immigration or emigration takes place
- random mating
- large population
- no selection occurs

List the characteristics of a population that is in Hardy-Weinberg equilibrium.

T/F: Evolutionary fitness is defined only by an organism's survival.

false

Drastic reduction in size results in a population losing genetic variation

Bottleneck effect

A few individuals of a population disperse and give rise to a new population

Founder effect

T/F: Natural selection is the result of evolution.

false

natural selection

Adult peppered moths (Biston betularia) come in a range of shades, ranging from light grey to dark black. Analysis has shown that the color of the moth is determined by genetics. In the age of industrialization, tree trunks were darkened as a result of pollution. It was observed that light-colored moths decreased in these polluted areas while the dark-colored moths increased. This is an example of natural selection .

Allopatric speciation

The differentiation of geographically isolated populations into distinct species.

sympatric speciation

The differentiation of populations within a common geographic area into distinct species.

Gametes of one species function poorly with the gametes of another species

Prevention of gamete fusion

Species reproduce at different times during the day or during different seasons

temporal isolation

Species have different mating rituals

Behavioral isolation

Hybrids that do not have the ability to produce offspring

Hybrid infertility

Embryos do not develop properly and may not be born or may die shortly afterwards

Hybrid inviability

Species occur in the same area, but they occupy different areas of the habitat

Ecological isolation

Species have different structures that prevent mating

Mechanical isolation

biological species concept

The ___________ is based on the principle that a species can interbreed and produce fertile offspring. Additionally, the gene pools of different species remain distinct.

Phylogenetic species concept

The ________________ defines the term species as groups of populations that evolve independently of other groups of populations.

T/F: Defining a species is a simple process, and scientists do not debate about the criteria for classifying organisms.

false

Which of the following answer choices describes the process of reinforcement in terms of reproductive isolation between two populations?

Selection that improves pre-zygotic isolating mechanisms until the two populations are separate species.

T/F: Genetic drift, including founder effects and bottleneck effects, and natural selection can lead to reproductive isolation. Reproductive isolation can lead to speciation.

true

Adaptive radiation describes a group of species that have recently evolved from a common ancestor; however, these species have adapted to different parts of the environment. Which of the following describes the main reason why adaptive radiation occurs on groups of islands?

Allopatric speciation is likely to occur, and the recently evolved species colonize other islands.

Gradualism

Small changes occur very slowly over geologically long periods of time

Punctuated equilibrium

Periods of little to no change and bursts of change over geologically short periods of time

phylogenetic trees

Biologists create diagrams called ____________ to hypothesize the evolutionary relationships between organisms.

ancestor

Reading phylogenetic trees is similar to reading a family tree: the root represents a(n) __________

decendants

The tips of the branches on a phylogenetic tree represent _____________

characters

In order to construct a phylogenetic tree, biologists collect data on the _____________ of organisms, which are recognizable, heritable features of an organism.

ancestral, derived

Heritable features can be classified as ___________ (a similarity among species that is inherited from the most recent common ancestor) or____________ (a similarity that arose more recently and is shared by only a subset of the species).

synapomorphies

Shared, derived characters—called _______________ —are informative in determining evolutionary relationships.

- physiology
- molecular data (DNA & protein sequences)
- morphology
- behavior

What can be used to determine variations between organisms when constructing a phylogeny?

A derived form of a trait that is shared by a group of related species

Synapomorphy

Organisms that are closely related, but not direct members of the group being studied

Outgroup

An organism and all of its descendants

Clade

- old-world monkeys share a common ancestor with humans
- gibbons are more closely related to orangutans than they are to humans
- chimpanzees are more closely related to humans than gorillas

What statements are supported by the phylogeny shown below?

Hypothesis 1

Applying the principle of parsimony, which hypothesis should be selected?

___________ is the study of biological diversity and the evolutionary relationships among organisms.

Systematics

__________ is the practice of placing species and/or groups of species into the taxonomic hierarchy.

classification

Monophyletic group

A group of organisms that form a clade (includes the most recent common ancestor and ALL of its descendants).

Polyphyletic Group

A group of organisms that does NOT contain the most recent common ancestor for all the members in the group.

Paraphyletic Group

A group of organisms that share a common ancestor although the group does NOT include all the descendants.

Which of the following terms describes when a shared character state is present but NOT inherited from a common ancestor?

Homoplasmy

Which of the following taxonomic groups could contain species that have similar phenotypes as a result of convergent evolution?

Polyphyletic

The Earth is ~ _________ years old

4.5 billion

In the early Earth's atmosphere, it is thought that __________ was lacking in the atmosphere

molecular oxegyn

Amino acids

What was found in the trap of the Miller-Urey apparatus that supports a hypothesis for the beginning of early life?

The Cambrian Explosion occurred 541 million years ago. This event resulted in an increase in _____.

Diversity of multicellular organisms

- rock layer C
- rock layer B
- rock layer A
- intrusion D
- fault E

Relative dating can provide estimates of the age of a fossil based on rock strata. Order the rock layers in the figure below from OLDEST to YOUNGEST.

________ means living together in close association. This theory provides a hypothesis for the origin of certain organelles in early __________ cells.

Endosymbiosis, eukariotic

Energy-producing bacteria may have come to reside within larger bacteria, eventually evolving into __________.

mitochondria

Photosynthetic bacteria may have come to reside within larger bacteria, eventually evolving into ___________.

cholroplasts

The chemical composition of the Earth's atmosphere has drastically changed over time. The emergence of photosynthetic organisms resulted in an increase in which of the following gases in the atmosphere?

Oxygen

ioactive decay is a useful tool for determining the age of fossils. For example, 14C will decay into 12C over time. If the ratio of 14C to 12C is 1:4 in a sample, what is the percentage of 14C in the sample? Enter your answer as a number.

20%

Which taxonomic rank includes more organisms than a Genus, but less than an Order?

Family

T/F: The Earth is still changing to this day.

True

Is emma sleepy?

yes