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OSU / Biology / IB 211 / What is a genome simple definition?

What is a genome simple definition?

What is a genome simple definition?

Description

School: Oregon State University
Department: Biology
Course: Principles of Biology
Professor: Anne petersen
Term: Summer 2016
Tags: prokaryotes, Bacteria, Biology: Ecology and Evolution, and natural selection
Cost: 50
Name: Biology 211
Description: Study guide that should be used alongside lecture notes and textbook notes in order to prepare for the first midterm.
Uploaded: 10/05/2017
9 Pages 9 Views 8 Unlocks
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Biology 211 Midterm Study Guide


What is a genome simple definition?



Chapter 1 Evolution, the themes of Biology, and Scientific Inquiry 1.1:​ ​The​ ​Study​ ​of​ ​Life​ ​Reveals​ ​Unifying​ ​Themes

- 5 Themes of Life

- Organization

- Information

- Energy and matter

- Interactions

- Evolution

- Theme: Organization

- Levels of Organization (also referred to as “Hierarchy of Life”) from largest to smallest - Biosphere

- Ecosystem

- Communities

- Populations

- Organisms

- Organs

- Tissues

- Cells

- Organelles

- Molecules

- Reductionism: Reduces complex systems to simpler concepts

- Emergent Properties: New properties that appear when moving between the different organization levels We also discuss several other topics like spa 204 study guide

- Occurs due to the difference in complexity between the levels

- System Biology: Approach to biology that focuses on the interactions within a whole biological system


Genomic and proteomic approaches are only viable through 3 research developments



- Can be used to study life at all levels

-Cells: Smallest unit of organization; basic unit of life

-Two main forms

-Eukaryotic Cells: Membrane enclosed organelles and nucleus

-Plants, animals

- Prokaryotic Cells: Organelles are not membrane enclosed, no nucleus and

typically smaller than eukaryotic cells

-Bacteria and Archaea

- Theme: Genetic Information

-DNA: Carries genetic information

-Genes: Unit of hereditary info

-Located in the DNA, or RNA, and contains a specific nucleotide sequence

-DNA directs the development of an organism by continuously replicating itself through cell division

-DNA molecules are made up of two polynucleotide strands in the shape of a double helix - Each strand contains 4 different bases, Adenine, Cytosine, Guanine and


Inductive reasoning



Don't forget about the age old question of the i = pat formula says that our environmental impacts (i) are the product of

Thymine whose sequence contains different genetic info based on their order If you want to learn more check out psy 505 ryerson
We also discuss several other topics like dr colin jones

- The sequence is the blueprint for making proteins

-DNA sequence: Specific order of nucleotides in a gene

-Gene expression: The process where the information encoded in the DNA directs the production of proteins

-Steps of gene expression

1. The sequence of nucleotides (in DNA) along a gene is transcribed into

mRNA.

2. The information from the mRNA are then translated in a linked chain of

amino acids.

3. The amino acid chain becomes a protein once it folds itself through a

process called protein folding. Once the protein folded itself, it now

functions as the protein it was coded for.

-Gene expression demonstrates that all forms of life essentially use the same

genetic code.

-Differences in organisms is due to the differences in its nucleotides

-Genomics

-Genomics: Systematic study of whole sets of genes, or DNA, and their interactions within a species as well as the genome comparisons between species. If you want to learn more check out nyucsc

-Genomes: Genetic material of an organism or virus and the complete set of an

organism/virus genes and noncoding nucleic acid sequences.

-Proteomics: Systematic study of sets of proteins and their properties.

-Properties are:

-Abundance

-Chemical modifications

-Interactions

-Proteome: The entire set of proteins expressed by a given cell, tissue, or

organism.

-Genomic and proteomic approaches are only viable through 3 research developments -High-throughput tech: Allows for rapid analysis of biological samples

-Bioinformatics: Use of computers, software and mathematical models to

process and integrate biological info from large data sets gained from high-throughput tools -Formation of interdisciplinary research teams

-Theme: Energy

-Producers: An organism that produces organic compounds through photosynthesis or chemosynthesis.

-Chemosynthesis: Synthesis of organic compounds from the energy released by reactions of inorganic chemicals.

-Occurs in some prokaryotes, including bacteria.

-Typically occurs due to absence or lack of sunlight

-Consumers: Organisms that eat other organisms or nonliving organic materials for energy.

-Theme: Interactions in biological systems

-Feedback regulation: The regulation of a process by its output or product

-Negative feedback: Response reduces initial stimulus; less end product

-Most common form of regulation in living systems

-See figure 1.11 in textbook for example

-Positive feedback: Response increases initial stimulus; more end product

-See pg. 11 in textbook for example Don't forget about the age old question of lbst 2101

-Climate change: Directional change in global climate that lasts for at least 3 decades.

Section​ ​1.2​ ​Evolution​ ​and​ ​the​ ​Unity/Diversity​ ​of​ ​Life

- Evolution: Changes in the genetic population over generations

- Can also be defined as “Descent with modifications”

- 3 domains of life

-Domain Bacteria

-Most diverse and widespread prokaryotes

-Domain Archaea

-Prokaryotes

-Domain Eukarya

4 Subgroups

-Kingdom Plantae

-Kingdom Fungi

-Kingdom Animalia

-Protists (Mostly unicellular eukaryotes)

-Charles Darwin’s Theory of Natural Selection

Based off of 3 observations

-Individuals in a population have varying traits, many of which, are heritable.

- A population can produce too many offsprings which results in some dying off due to limited resources in an environment resulting in competition.

- Species are generally suited to their environment (adaptation)

-Natural selection: Traits that are beneficial to survival within a specific environment are more likely to be passed onto future generations.

-Darwin believed that natural selection over a long period of time can cause a

species to speciate.

Section​ ​1.3​ ​Observations​ ​and​ ​Forming/Testing​ ​hypothesis

- Inquiry: Search for information and explanation often on specific questions.

- Hypothesis: A testable explanation based on observations and inductive reasoning. - Inductive reasoning: Generalizations that are based on a large number of specific observations. - Deductive reasoning: Specific results are predicted from a general premise. - “If…..Then” logic

- Process of inquiry:

1. Making observations

2. Form hypothesis

3. Test hypothesis

- Controlled experiment: Experiment comparing an experimental group with a control group. - Independent variable: Variable manipulated by researchers.

- Dependent variable: Variable being measured

- Qualitative data: Recorded description

- Quantitative data: Numerical measurements

- Scientific theory: A broad explanation that generates new hypotheses and is supported by a large amount of evidence/data.

Chapter 22 Descent With Modification: A Darwinian View of Life

Section​ ​22.1​ ​The​ ​Darwinian​ ​Revolution

- Fossils- A preserved remnant of an organism that lived in the past.

- Most fossils are located in compressed sedimentary rocks (strata).

- Based on the location of the fossil in the strata, paleontologists can determine what type of organisms were alive during that time.

- Hutton and Lydell’s influence on Darwin

- Hutton believed that Earth’s geologic features happened due to gradual change - Lydell added onto Hutton proposal and believed that the process of gradual change happens at a constant rate.

- This led Darwin to think that the Earth has to be more than the accepted age of more than a few thousand years and that the slow, gradual changes could have caused dramatic biological changes.

- Lamarck’s Hypothesis of Evolution

- Lamarck discovered a link between certain fossils resembling living species.

- Found line of descent of living species to old fossils

- Explained his findings using two accepted principle:

- Use and disuse: Parts of the body that were used more often would become

larger and stronger, while parts used less often would disappear.

- Inheritance of acquired characteristics: Organisms could pass on modifications (from the use and disuse principle) to future offsprings.

- Lamarck believed that evolution happened because organisms have an innate drive to be more complex.

- Darwin reject his ideas but believed in the inheritance of acquired characteristics Section​ ​22.2​ ​Descent​ ​With​ ​Modifications

- Adaptation: Inherited traits/characteristics of an organisms that helps it survive and reproduce within an environment.

- Darwin later believed that adaptation and the origin of new species were two related processes.

- Darwin explained how adaptation came to be using his theory of natural selection - See Figure 22.6 and pg 471 to understand where Darwin got his idea for

adaptation

- Darwin and the Galapagos Island

- After spending time at the Galapagos, Darwin hypothesized that the organisms living there must have originally come from the mainland and over time speciated, creating a wide diversity of species. - “The Origin of Species”

- Darwin’s book about “Descents with modifications” by natural selection that explains the effects of it on the diversity of nature.

- Used the process of artificial selection to support his claim of natural selection - Artificial selection: Human selectively breeding domesticated plants and

animals to increase the occurrence of a desired trait.

- With the background of artificial selection, Darwin then argues that the same

process happens in nature through 2 observation to support his idea of natural selection 1. Members of a population inherits varying traits. Inherited traits

that allows them to survive and reproduce better, within a

specific environment, will have a higher probability of passing on

those traits.

2. All species produce more offspring than their environment can

handle leading to many of the offspring to die. This leads to the

accumulation of favorable traits within a population over

generations

Individuals​ ​do​ ​not​ ​evolve,​ ​only​ ​the​ ​population​ ​evolves​! 

Natural​ ​selection​ ​can​ ​only​ ​occur​ ​if​ ​there’s​ ​a​ ​variation​ ​of​ ​traits​ ​within​ ​a​ ​population.​ ​ ​Population​ ​that are​ ​genetically​ ​identical​ ​with​ ​no​ ​variation​ ​cannot​ ​evolve​ ​through​ ​natural​ ​selection. 

Traits​ ​are​ ​only​ ​favorable​ ​within​ ​a​ ​specific​ ​environment.

Section​ ​22.3​ ​Evolution​ ​is​ ​Supported​ ​by​ ​Scientific​ ​Evidence

- Homology: Similarity in characteristics due to a common, shared ancestry

- Homologous structure: Similar structures in different species due to a common ancestry

- Vestigial structure: Features of an organism that once had a function in the organism’s ancestry. - Evolution Tree: Diagram that shows the hypothesis about the evolutionary relationship among groups of organisms.

- Convergent Evolution: Evolution of similar features in independent evolutionary lineages. - Analogous: Having characteristics that are similar due to convergent evolution, not because of homology

- Biogeography: Study of the past and present geographic distributions of species. - Endemic: A species confined to a specific geographic area.

- Pangaea: Supercontinent

Chapter 26 Phylogeny and the Tree of Life

Section​ ​26.1​ ​Phylogenies​ ​Show​ ​Evolutionary​ ​Relationships

- Phylogeny: Evolutionary history of species

- Focuses on individual species as well as groups of related species

- Taxonomy: Naming and classifying forms of life

- Taxon/taxa: Named group in hierarchical classification system; a taxonomic unit - Binomial: Term for the two part, latinized format for naming a species.

Genus: Category above species; first part of the binomial name of a species

Specific epithet: Naming of a species within a genus; second part of the binomial name

- Hierarchical Classifications

- Domain

- Kingdom

- Phyla

- Class

- Order

- Family

- Genera

- Species

- Phylogenetic Tree: Branching diagram that represents the evolutionary relationship between organisms.

- Branch point: Shows the split of two or more taxa from a common ancestor

- Sister taxa: Organisms that share an immediate common ancestor; shows closest relatives of an organism.

- Rooted: Branch point representing the common ancestor of all taxa on a tree.

- Basal taxon: The earliest point where an organism, or group of, evolutionary lineage splits off.

Section​ ​26.2​ ​Phylogenies​ ​are​ ​Inferred​ ​from​ ​Morphological​ ​and​ ​Molecular​ ​Data

- Analogy: Similarity between two species due to convergent evolution, not due to the sharing of a common ancestor

- If two organisms share most of the same nucleotide sequence, then it is likely that they are homologous

- If two, or more organisms, share similar appearances, it does not make them related unless they have very similar gene sequencing.

- To see more about how DNA affects phylogenies see Figure 26.7 and 26.8. Section​ ​26.3​ ​Shared​ ​Characters​ ​are​ ​Used​ ​to​ ​Construct​ ​Phylogenetic​ ​Trees

- Cladistic: Approach to systematics where organisms are placed into clades based on common descents

- Clade: A group of species that include an ancestral species and all of its descendants. - Equivalent to a monophyletic group

- Monophyletic: A group of taxa that consists of a common ancestor and descendants. - Equivalent to a clade

- A taxon is equivalent to a clade only if it’s monophyletic

- Paraphyletic: A group of taxa with a common ancestor and some of its descendants. - Polyphyletic: A group of taxa with distantly related organisms but does not include their common ancestor.

- The common ancestor would not be included in the same group as its descendants - Biologists tend to avoid defining polyphyletic groups instead choosing to reclassify the group whenever possible.

- Shared ancestral character: A character which is shared by members of a clade but originated from an ancestor not from that clade.

- Shared derived character: An evolutionary character that is unique to a particular clade. - Can also refer to a loss of a character

- Outgroup: Refers to a species’, or group of, lineage that is not part of the ingroup. - Ingroup: Refers to a species, or group of, whose relationship are being analyzed. The branch length on a phylogenetic tree represents the amount of genetic change that occurred in a species compared to its ancestor.

- Longer length= more genetic change

- Shorter length= less genetic change

- Maximum Parsimony: A principle where the simplest explanation that is consistent with the facts should be used

- For a morphology tree, it is the tree with the least amount of evolutionary change - For a phylogenetic tree, it is the tree with the fewest base change

- Maximum likelihood: An approach that identifies the tree that is the most likely to have produced a certain set of DNA based on how DNA sequences change over time.

- Phylogenetic bracketing: Predicting characters shared by two groups of closely related organisms that would appear on their common ancestor and its descendants.

Chapter 27 Bacteria and Archaea

Section​ ​27.4​ ​Prokaryotic​ ​Diversity

Horizontal gene transfer is an important factor to the evolution of prokaryotes.

- Horizontal gene transfer: Transmission of DNA between species and possibly non-related species; can transfer traits.

Characteristics of prokaryotic cells

- Very small cells (typically around 0.1–5.0 µm) 

- No complex membrane-bound organells

- 3 common shapes: spherical, rod-shaped, and spiral

Prokaryotes are separated into bacteria and archaea.

- Bacteria

- Vast majority of prokaryotes

- Every major nutrition and metabolism includes bacteria

- Bacteria within a taxonomic group may contain species with many different nutritional modes.

- Archaea

- Less common

- Located in extreme environments

The firsts prokaryotes to be named archaea were extremophiles

- Extremophiles: Organisms that live in extreme environmental conditions.

- Extreme Halophiles: Organisms that live in highly saline environment

- Extreme Thermophiles: Organism that live in hot environment

- Most archaea live in moderate environments

- Methanogens: Organisms that produce methane as a waste product due to the way they obtain energy.

- Most oxidize H2 using CO2 as a way to gain energy

- Some are extremophiles

- All of them are poisoned by O2

Section​ ​27.5​ ​Prokaryotes​ ​Play​ ​A​ ​Crucial​ ​Role​ ​in​ ​the​ ​Biosphere

If all prokaryotes disappeared, the survival rate for other species would be very low.

Chemical Recycling

- Decomposers: Breaks down dead organisms and waste products to convert them into inorganic materials

- Some prokaryotes can create organic materials for other organisms to use

Ecological Interactions

- Symbiosis: Ecological relationship between two organisms of different species that live together in close contact

- Host: The larger organism in a symbiotic relationship; often provides a home and food source for the symbiont

- Symbiont: The smaller organism that lives in or on its host

- Can result in mutualism

- Mutualism: Ecological interaction that benefits the interacting organisms

- Commensalism: One organism benefits while the other receives/provides nothing. - Parasitism: Interaction where the parasite feeds upon the host.

- Parasite: Organisms that feed on the host

- Pathogens: Organisms or viruses that causes disease

Section​ ​27.6​ ​Prokaryotes​ ​can​ ​be​ ​both​ ​Harmful​ ​and​ ​Beneficial​ ​to​ ​Humans

Mutualistic Bacteria

- Most live in our intestines

- Some can signal cells to do something (see pg 587).

Pathogenic Bacteria

- Usually causes illnesses by producing poisons (exotoxins and endotoxins)

- Exotoxins: Toxic protein whose symptoms continues even when the pathogenic bacteria/organisms is no longer present

- Endotoxins: Toxin from certain gram-negative bacteria that are released from the outer membrane only when the bacteria dies.

Prokaryotes in Research and Technology

- CRISPR-Cas9 system: A technique for editing genes in living cells using a bacterial protein called Cas9 and a RNA guide from the gene sequence of interest.

- Bioremediation: Use of organisms to restore polluted and degraded ecosystems

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