Organismal Test 1 review
Chapter 1. Introduction: Evolution and the Foundations of Biology
Read the Overview: Inquiring about life. Use figure 1.1. and caption. Why are some mice light and some dark? Which are dark and which are pale? Are these same species or different species? What is adaptation? Camouflage? Evolution? Are adaptations inherited or acquired?
Light and Dark Mice: The coloration of mice can vary due to genetic factors and environmental adaptations. Dark mice are often found in darker environments, while light mice may inhabit lighter areas.
Species: These mice can be the same species exhibiting different color morphs or different species altogether.
Adaptation: A trait that enhances survival and reproduction in a specific environment.
Camouflage: A form of adaptation where an organism blends into its environment to avoid predation.
Evolution: The process through which species change over time through natural selection.
Inherited vs. Acquired: Adaptations are typically inherited traits, not acquired during an organism's lifetime.
What are some questions asked by biologists? Know the three concepts and how biologists use these as a framework to make sense of life’s complexity and diversity:
Biologists often ask questions related to:
Structure and Function: How do the structures of organisms relate to their functions?
Unity and Diversity: What are the similarities and differences among various life forms?
Change Over Time: How do species evolve and adapt to their environments?
These concepts help biologists understand life's complexity and diversity by providing a framework for studying relationships, adaptations, and evolutionary processes.
Know the 5 big ideas, the 5 unifying themes in the study of life.
Evolution: The process by which species change over time through natural selection and genetic variation.
Energy and Matter: Life depends on the transfer and transformation of energy and matter, including photosynthesis and cellular respiration.
Information: Genetic information is stored in DNA and is crucial for the development, functioning, and reproduction of organisms.
Interactions: Organisms interact with each other and their environments, influencing ecosystems and biological communities.
Structure and Function: The structure of biological molecules, cells, and organisms is closely related to their function, impacting how they operate and survive.
Under the theme Organization be sure to understand figure 1.3 very well. Be sure to be able to zoom in from outer space and identify the various levels in the hierarchy in the right sequence, or zoom out from molecules all the way up. Define and understand each level with all examples and illustrations given. Be sure to be able to define biosphere, ecosystem, community, species, population, organism, organ, tissue, cell, organelle, molecule.
Biosphere: The global sum of all ecosystems; the zone of life on Earth.
Ecosystem: A community of living organisms and their physical environment interacting as a system.
Community: A group of different species living together in one area.
Population: A group of individuals of the same species living in a specific area.
Organism: An individual living entity that can function independently.
Organ: A collection of tissues that perform a specific function (e.g., heart).
Tissue: A group of similar cells that work together to perform a function (e.g., muscle tissue).
Cell: The basic unit of life; the smallest structural and functional unit of an organism.
Organelle: Specialized structures within a cell that perform specific functions (e.g., mitochondria).
Molecule: A group of atoms bonded together, representing the smallest fundamental unit of a chemical compound (e.g., DNA).
What is Reductionism and how is this approach different from the approach Systems Biologists use?
Reductionism is an approach in science that breaks down complex systems into their simpler components to understand their function and behavior. It focuses on individual parts, often at a molecular or cellular level.
Systems Biology, on the other hand, emphasizes the interactions and relationships between components within a biological system. It studies the system as a whole, considering how parts work together to produce emergent properties.
In summary:
Reductionism: Analyzes parts individually.
Systems Biology: Examines interactions and the whole system.
What are emergent properties? Are they unique to life? Learn the two examples of questions systems biologists ask.
Definition: Emergent properties are characteristics of a system that arise from the interactions of its components, rather than from the properties of the individual parts.
Uniqueness to Life: While many emergent properties are observed in biological systems, they are not unique to life; they can also occur in non-living systems (e.g., weather patterns).
How do interactions between different species affect ecosystem stability?
What are the effects of genetic variations on population dynamics?
Under Structure and Function, know the two examples of how structure is perfectly correlated with function.
Bird Wings: The structure of bird wings, with their lightweight bones and feathers, allows for efficient flight. The shape and flexibility enable lift and maneuverability.
Human Heart: The heart's structure, with its four chambers and valves, is designed to efficiently pump blood throughout the body, ensuring proper circulation and oxygen delivery.
What is Cell? Know examples of actions of organisms that are based on cellular activities. How is a global process like recycling of carbon an ultimate product of cellular function?
A cell is the basic structural and functional unit of all living organisms. Examples of actions based on cellular activities include:
Metabolism: Energy production through cellular respiration.
Growth: Cell division and differentiation.
Response to stimuli: Movement or behavior changes in response to environmental factors.
The global process of carbon recycling is an ultimate product of cellular function as cells in plants (through photosynthesis) absorb carbon dioxide, while cellular respiration in animals releases it, maintaining the carbon cycle essential for life.
What are some features all cells share? Distinguish between prokaryotic and eukaryotic cells using figure 1.4. What is the size difference? Practice using the measuring scale in images taken under a microscope. How big are bacterial cells? How big are most of your cells?
Cell membrane
Cytoplasm
Ribosomes
Genetic material (DNA/RNA)
Prokaryotic Cells:
No nucleus
Smaller (0.1 - 5.0 µm)
Simple structure (e.g., bacteria)
Eukaryotic Cells:
Nucleus present
Larger (10 - 100 µm)
Complex structure (e.g., plant and animal cells)
Typically range from 0.5 to 5.0 µm.
Generally range from 10 to 30 µm.
Please know the following although it isn’t covered in the chapter: 1 meter is 3.3 feet; 1/1000th of a meter is a millimeter (mm); 1/1000th of a mm is a micron or micrometer (µm); 1/1000th of a micron is a nanometer (nm). Molecules are measured in nm, for example, the DNA molecule is about 2 nm in width.
Under the theme of Information, what is DNA? Use figure 1.5. How big are those cells?
DNA Overview: DNA (deoxyribonucleic acid) is the hereditary material in all known living organisms and many viruses. It carries genetic instructions for development, functioning, growth, and reproduction.
Cell Size: Typical human cells range from about 10 to 30 micrometers in diameter. However, sizes can vary significantly depending on the cell type.
What are genes? Use figure 1.6 to know that inherited DNA directs the development of an offspring of two parents.
Genes are segments of DNA that contain the instructions for the development, functioning, growth, and reproduction of organisms.
They are inherited from parents and play a crucial role in determining traits and characteristics of offspring.
Inherited DNA directs these processes, ensuring that genetic information is passed down through generations.
What are nucleotides and what are the 4 types? How does DNA encode information? Use the rat, tar, art analogy to explain this idea:
Nucleotides are the basic building blocks of nucleic acids, such as DNA and RNA. Each nucleotide consists of three components: a phosphate group, a sugar (deoxyribose in DNA), and a nitrogenous base.
The 4 types of nucleotides in DNA are:
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
DNA Encoding Information: DNA encodes information through the sequence of its nitrogenous bases. The analogy of "rat," "tar," and "art" illustrates how different arrangements of the same letters (nucleotides) can create distinct meanings (genes). Just as rearranging letters forms different words, varying nucleotide sequences produce different proteins and functions in organisms.
It is important for you to understand how the nucleotide sequence of a gene is used as a blueprint to make a specific protein. Know that proteins are molecular workhorses in a cell, and that each protein is a sequence of various amino acids folded in particular three-dimensional shapes. The sequence and shape determines protein function.
What is gene expression? Know crystallin, transcription, translation, mRNA:
Gene Expression is the process by which information from a gene is used to synthesize a functional gene product, typically proteins.
Crystallin: A type of protein found in the lens of the eye, crucial for maintaining transparency and refractive properties.
Transcription: The process of copying a segment of DNA into mRNA.
Translation: The process where ribosomes synthesize proteins using the mRNA sequence.
mRNA (messenger RNA): A type of RNA that carries genetic information from DNA to the ribosome, where proteins are synthesized.
How is the genetic code used to discern evolutionary relationships? How do we know that we are very closely related to Chimpanzees and only distantly related to mice and grasses?
The genetic code, composed of DNA sequences, is used to discern evolutionary relationships through comparative genomics. By analyzing similarities and differences in DNA sequences among species, scientists can construct phylogenetic trees that illustrate evolutionary lineages.
Humans and chimpanzees share approximately 98-99% of their DNA, indicating a recent common ancestor. In contrast, humans share about 85% of their DNA with mice and much less with grasses, reflecting more distant evolutionary relationships. These comparisons help establish the degree of relatedness among species.
What is the field of Genomics? What is a genome? How large is your genome? What is proteomics and what is a proteome? Learn, and please don’t memorize.
Definition: The process by which information from a gene is used to synthesize a functional gene product, typically proteins.
Key Components:
Crystallin: A type of protein found in the lens of the eye, important for transparency and refractive properties.
Transcription: The process of copying a segment of DNA into mRNA.
Translation: The process where ribosomes synthesize proteins using mRNA as a template.
mRNA: Messenger RNA, a type of RNA that conveys genetic information from DNA to the ribosome.
Field: The study of genomes, the complete set of DNA within an organism.
Genome Size: Human genome consists of approximately 3 billion base pairs.
Definition: The large-scale study of proteins, particularly their functions and structures.
Proteome: The entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time.16.
What are the three important research developments that have made genomic and proteomic approaches possible in recent decades? What is bioinformatics? Know the example I mentioned in lecture about the race to make a new vaccine.
Next-Generation Sequencing (NGS): Allows rapid sequencing of DNA, making genomic studies more efficient.
Mass Spectrometry: Enhances proteomic analysis by identifying and quantifying proteins in complex samples.
CRISPR-Cas9 Technology: Enables precise gene editing, facilitating functional genomics research.
Bioinformatics is the application of computer technology to manage and analyze biological data, particularly in genomics and proteomics.
Unknown.
How have humans affected the environment? Know those two paragraphs on climate change well with all those statistics and examples. (Starting with “Like other organisms, we humans interact….”). Approximately what % of CO2 released by fossil fuels remains in the atmosphere? How are organisms affected by this human-caused climate change? Specifically, how are Sceloporus lizards affected by this? Use fig. 1.11 and caption. What is extinction?
Approximately 50% of CO2 released by fossil fuels remains in the atmosphere.
Organisms are affected by climate change through habitat loss, altered food availability, and changing weather patterns.
Sceloporus lizards are particularly impacted as rising temperatures can affect their metabolism, reproduction, and survival rates. They may struggle to find suitable habitats as their preferred environments change.
Extinction is the permanent loss of a species, occurring when the last individual of that species dies, often due to environmental changes, habitat destruction, or human activities.
What are the three Domains? Know all examples and characteristics in that figure. Why don’t we classify protists under their own Kingdom?
Bacteria
Prokaryotic, unicellular organisms.
Peptidoglycan cell wall.
Diverse metabolic pathways.
Archaea
Prokaryotic, unicellular organisms.
Unique membrane lipids and no peptidoglycan.
Often extremophiles (e.g., thermophiles, halophiles).
Eukarya
Eukaryotic organisms (cells with a nucleus).
Includes kingdoms: Animalia, Plantae, Fungi, and Protista.
Complex cellular structures.
Protists are not classified under their own kingdom due to their diverse characteristics and evolutionary relationships, which make them more similar to multiple kingdoms rather than a distinct group.
Learn about Charles Darwin under that subtitle. What’s the famous book he wrote? What’s Descent with Modification? Why is it such an insightful phrase? Explain the two main points Darwin articulated in his book.
Famous Book: Darwin wrote "On the Origin of Species" in 1859.
Descent with Modification: This concept refers to the idea that species evolve over time, with changes passed down through generations.
Insightful Phrase: It highlights the process of evolution and the common ancestry of life forms.
Two Main Points:
Natural Selection: The mechanism by which individuals with favorable traits are more likely to survive and reproduce.
Variation: The existence of differences among individuals in a population, which is crucial for evolution.
Learn how birds show unity and diversity using figure 1.15. Be sure to know the caption in all figures.
What were Darwin’s three essential observations that helped him shape the theory of Natural Selection?
Darwin's three essential observations for the theory of Natural Selection are:
Variation: Individuals within a species show variation in traits, such as size, color, and shape.
Inheritance: Some of these variations are heritable and can be passed on to the next generation.
Differential Survival and Reproduction: Individuals with advantageous traits are more likely to survive and reproduce, leading to the gradual evolution of the species.
How is the human arm an example to illustrate the unity and diversity of life?
The human arm exemplifies unity and diversity in life through its anatomical structure and evolutionary significance.
Unity: All vertebrates share a similar bone structure (humerus, radius, ulna) due to common ancestry, illustrating the concept of homologous structures.
Diversity: Different species have adapted their limb structures for various functions (e.g., wings in birds, flippers in whales), showcasing how evolution shapes form and function based on environmental needs.
This duality highlights both the shared heritage and the adaptive variations among living organisms.
How can geographical separation split a species into two species? Use the example in my lecture on the squirrels of the Grand Canyon.
Geographical separation can lead to speciation through a process called allopatric speciation.
In the case of the Grand Canyon squirrels, the canyon acts as a barrier, dividing a single squirrel population into two isolated groups. Over time, these groups experience different environmental pressures and genetic drift, leading to adaptations that make them distinct. Eventually, reproductive isolation occurs, resulting in the emergence of two separate species.
How can the Tree of Life be used to illustrate that all life descended from unicellular prokaryotes?
The Tree of Life illustrates the evolutionary relationships among all living organisms, showing that they share a common ancestor. By tracing back the branches, we can see that all complex life forms, including plants and animals, diverged from unicellular prokaryotes (like bacteria). This representation highlights the concept of common descent, demonstrating how diverse life evolved from simple, single-celled organisms over billions of years through processes like natural selection and genetic variation.
What is science? What is inquiry?
Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe. It involves observation, experimentation, and analysis.
Inquiry is the process of seeking information, understanding, or knowledge through questioning, investigation, and exploration. It often involves formulating hypotheses and conducting experiments to gather evidence.
The enterprise of science begins with what? What are data? What are the two types of data? Give examples from Jane Goodall’s work on Chimpanzees.
The enterprise of science begins with observation and questioning.
Data are facts and statistics collected for analysis.
The two types of data are:
Qualitative Data: Descriptive information (e.g., behaviors of chimpanzees, such as grooming or social interactions).
Quantitative Data: Numerical information (e.g., the number of chimpanzees in a group or the frequency of specific behaviors).
Jane Goodall's work includes observing social behaviors (qualitative) and counting individuals in her study groups (quantitative).
What is a hypothesis? What kind of reasoning is involved when you form a hypothesis? For a hypothesis to be valuable it has to be ______.
A hypothesis is a testable statement or prediction about the relationship between variables.
The reasoning involved in forming a hypothesis is typically inductive reasoning, where observations lead to generalizations.
For a hypothesis to be valuable, it has to be falsifiable, meaning it can be proven wrong through experimentation or observation.
How can you test a hypothesis? (two ways).
Conduct experiments: Manipulate variables in a controlled environment to observe outcomes.
Perform observational studies: Collect data in natural settings to identify patterns or correlations.
What is a theory? What would you say to a student who rejects evolution as “just a theory”?
A theory in science is a well-substantiated explanation of an aspect of the natural world, based on a body of evidence.
What are the 4 ways a scientific theory are different from a hypothesis?
Definition:
Hypothesis: A testable prediction or educated guess about the relationship between variables.
Theory: A well-substantiated explanation of an aspect of the natural world, based on a body of evidence.
Evidence:
Hypothesis: Requires testing and experimentation to gather evidence.
Theory: Supported by extensive evidence and has withstood repeated testing.
Scope:
Hypothesis: Narrow in scope, often specific to a particular experiment.
Theory: Broad in scope, explaining a wide range of phenomena.
Status:
Hypothesis: Considered provisional and subject to rejection or modification.
Theory: Generally accepted within the scientific community until disproven or revised.
Know the 3 key concepts
Learn the overview using fig. 19.1 What does this moth and its Lepidopteran relatives teach us about the unity and diversity of life?
Know the 3 key observation about life we can derive from this example.
What are the 2 ways we can define evolution? (One: Descent with modification, Two: change in genetic composition of a population from generation to generation).
Concept 19.1. The Darwinian revolution challenged traditional views of a young earth inhabited by unchanging species
Know about Aristotle’s Scala Naturae and the ladder of life.
Learn the role played by fossils in changing of ideas over time. Know figure 19.3. What is paleontology?
Know Lamarck’s hypothesis. When did he publish it? Know the principle of use and disuse and inheritance of acquired characteristics. How did he use the giraffe to explain these? Was he right? Why does he deserve rightful recognition? Know figure 19.4.
Concept 19.2. Descent with modification by natural selection explains adaptations of organisms and the unity and diversity of life
Know all about the voyage of the Beagle. Use figure 19.5. Where and when did they sail? Where are the Galapagos Islands?
Know the para under Darwin’s focus on Adaptation. Know fig. 19.6.
Why was he reluctant to publish his findings? Who was Alfred Russell Wallace? Where were his travels? Know the para starting with “In June 1858…” that explains their complicated relationship. Use figure 19.7.
Be sure to watch the The Origin of Species: The Making of a Theory video. It is an excellent summary of what these two great naturalists accomplished and found out. Please use the transcript PDF available in the HHMI website (link in Blackboard) and study that also after watching the film. Be sure to understand the location and significance of the Wallace’s Line. What kind of mammals predominate east of this line? West of this line?
Ideas from The Origin of Species
We went over the first two paragraphs including figure 19.8. Know these and explain the tree of life as Darwin did. See a real life example in fig. 19.9.
Artificial Selection, Natural Selection, and Adaptation
Use fig. 19.10 to articulate how Darwin used artificial selection as an analogy for natural selection.
Know the two observations and two inferences. Use figs. 19.11 and 19.12 and their captions.
Key Features of Natural Selection
Know the three main ideas (bulleted points) using fig. 19.13 and its caption.
Know the three key points about Natural Selection under fig 19.13. Can individuals evolve? In a given heritable trait, if all individuals have it identically, can evolution occur? Why or why not? Can a trait be an asset at some time or place and then become a liability?
Concept 19.3. Evolution is supported by an overwhelming amount of scientific evidence
Read the first two paras. What 4 types of data do we cover here that document evolution and illuminate how it occurs?
Direct observations of evolutionary change
Learn in depth the soapberry bug example and the field study to test the hypothesis. Can selection for beak length occur only one way? Why or why not? Be sure to thoroughly know the graph under Results. How did they measure beak lengths before introductions? How rapid was this evolutionary change in c. Florida?
Also know in depth the important issue of bacterial resistance to antibiotics. What are MRSA and USA300? Know figure 19.17. What are the nonblue areas and what do they signify? How big is the genome?
Know the story of how it began in 1943 and how it progressed (first 3 paras)
Read the para that starts with “The S. aureus and soapberry bug examples……” to learn the three key points about natural selection. These are points we have covered before and this helps reinforcing those important points. Remember, natural selection cannot cause variations; and individuals don’t evolve, populations do; and a favorable trait today or in some place may not be so tomorrow or in another place.
Homology
What is homology? Use fig. 19.16 for an excellent example of anatomical homology; and fig. 19.17 for anatomical homology. Be sure to know the captions.
What are vestigial structures? Know the examples from snakes and fishes.
A Different Cause of Resemblance: Convergent Evolution
What is it? Is it common? Use fig. 19.18. What is the opposite of homologous? So the “wings” (patagium) of the sugar glider and flying squirrel are said to be analogous organs.
The Fossil Record
Know the stickleback example and what it means.
Use fig. 19.19 to know how ankle bones provide insights into cetacean ancestry. Be sure to know the caption well.
Also use fig. 19.20 to know how the ancestors of whales started as 4-legged terrestrial (=land-based) mammals and them progressively evolved the streamlined shape that cetaceans have for movement in water. Know how the highlighted organisms adapted by modifying their hindlimbs using the color coded bones.
Biogeography
Know continental drift, Pangaea, when they occurred. Know the Equus example to learn how we can make predictions of where fossils of different groups of organisms might be found.
What is endemic? Why do islands have a lot of endemics? Why do islands like the Galapagos have clusters of closely related species? Why do two islands with similar environments in distant parts of the world (like Hawaii and Galapagos) don’t share similar species, but have species more allied to nearest mainland?
Is this JUST A THEORY?
How do scientists use this word compared to popular usage?
Can predation result in natural selection for color patterns in guppies? This is an important section. Learn it well in its entirety, including the figure and experimental design and the graph. How many generations and months passed for this change to occur? Where did this study take place? What are the two predators? Etc etc.
Chapter 1. Introduction: Evolution and the Foundations of Biology
Read the Overview: Inquiring about life. Use figure 1.1. and caption. Why are some mice light and some dark? Which are dark and which are pale? Are these same species or different species? What is adaptation? Camouflage? Evolution? Are adaptations inherited or acquired?
Light and Dark Mice: The coloration of mice can vary due to genetic factors and environmental adaptations. Dark mice are often found in darker environments, while light mice may inhabit lighter areas.
Species: These mice can be the same species exhibiting different color morphs or different species altogether.
Adaptation: A trait that enhances survival and reproduction in a specific environment.
Camouflage: A form of adaptation where an organism blends into its environment to avoid predation.
Evolution: The process through which species change over time through natural selection.
Inherited vs. Acquired: Adaptations are typically inherited traits, not acquired during an organism's lifetime.
What are some questions asked by biologists? Know the three concepts and how biologists use these as a framework to make sense of life’s complexity and diversity:
Biologists often ask questions related to:
Structure and Function: How do the structures of organisms relate to their functions?
Unity and Diversity: What are the similarities and differences among various life forms?
Change Over Time: How do species evolve and adapt to their environments?
These concepts help biologists understand life's complexity and diversity by providing a framework for studying relationships, adaptations, and evolutionary processes.
Know the 5 big ideas, the 5 unifying themes in the study of life.
Evolution: The process by which species change over time through natural selection and genetic variation.
Energy and Matter: Life depends on the transfer and transformation of energy and matter, including photosynthesis and cellular respiration.
Information: Genetic information is stored in DNA and is crucial for the development, functioning, and reproduction of organisms.
Interactions: Organisms interact with each other and their environments, influencing ecosystems and biological communities.
Structure and Function: The structure of biological molecules, cells, and organisms is closely related to their function, impacting how they operate and survive.
Under the theme Organization be sure to understand figure 1.3 very well. Be sure to be able to zoom in from outer space and identify the various levels in the hierarchy in the right sequence, or zoom out from molecules all the way up. Define and understand each level with all examples and illustrations given. Be sure to be able to define biosphere, ecosystem, community, species, population, organism, organ, tissue, cell, organelle, molecule.
Biosphere: The global sum of all ecosystems; the zone of life on Earth.
Ecosystem: A community of living organisms and their physical environment interacting as a system.
Community: A group of different species living together in one area.
Population: A group of individuals of the same species living in a specific area.
Organism: An individual living entity that can function independently.
Organ: A collection of tissues that perform a specific function (e.g., heart).
Tissue: A group of similar cells that work together to perform a function (e.g., muscle tissue).
Cell: The basic unit of life; the smallest structural and functional unit of an organism.
Organelle: Specialized structures within a cell that perform specific functions (e.g., mitochondria).
Molecule: A group of atoms bonded together, representing the smallest fundamental unit of a chemical compound (e.g., DNA).
What is Reductionism and how is this approach different from the approach Systems Biologists use?
Reductionism is an approach in science that breaks down complex systems into their simpler components to understand their function and behavior. It focuses on individual parts, often at a molecular or cellular level.
Systems Biology, on the other hand, emphasizes the interactions and relationships between components within a biological system. It studies the system as a whole, considering how parts work together to produce emergent properties.
In summary:
Reductionism: Analyzes parts individually.
Systems Biology: Examines interactions and the whole system.
What are emergent properties? Are they unique to life? Learn the two examples of questions systems biologists ask.
Definition: Emergent properties are characteristics of a system that arise from the interactions of its components, rather than from the properties of the individual parts.
Uniqueness to Life: While many emergent properties are observed in biological systems, they are not unique to life; they can also occur in non-living systems (e.g., weather patterns).
How do interactions between different species affect ecosystem stability?
What are the effects of genetic variations on population dynamics?
Under Structure and Function, know the two examples of how structure is perfectly correlated with function.
Bird Wings: The structure of bird wings, with their lightweight bones and feathers, allows for efficient flight. The shape and flexibility enable lift and maneuverability.
Human Heart: The heart's structure, with its four chambers and valves, is designed to efficiently pump blood throughout the body, ensuring proper circulation and oxygen delivery.
What is Cell? Know examples of actions of organisms that are based on cellular activities. How is a global process like recycling of carbon an ultimate product of cellular function?
A cell is the basic structural and functional unit of all living organisms. Examples of actions based on cellular activities include:
Metabolism: Energy production through cellular respiration.
Growth: Cell division and differentiation.
Response to stimuli: Movement or behavior changes in response to environmental factors.
The global process of carbon recycling is an ultimate product of cellular function as cells in plants (through photosynthesis) absorb carbon dioxide, while cellular respiration in animals releases it, maintaining the carbon cycle essential for life.
What are some features all cells share? Distinguish between prokaryotic and eukaryotic cells using figure 1.4. What is the size difference? Practice using the measuring scale in images taken under a microscope. How big are bacterial cells? How big are most of your cells?
Cell membrane
Cytoplasm
Ribosomes
Genetic material (DNA/RNA)
Prokaryotic Cells:
No nucleus
Smaller (0.1 - 5.0 µm)
Simple structure (e.g., bacteria)
Eukaryotic Cells:
Nucleus present
Larger (10 - 100 µm)
Complex structure (e.g., plant and animal cells)
Typically range from 0.5 to 5.0 µm.
Generally range from 10 to 30 µm.
Please know the following although it isn’t covered in the chapter: 1 meter is 3.3 feet; 1/1000th of a meter is a millimeter (mm); 1/1000th of a mm is a micron or micrometer (µm); 1/1000th of a micron is a nanometer (nm). Molecules are measured in nm, for example, the DNA molecule is about 2 nm in width.
Under the theme of Information, what is DNA? Use figure 1.5. How big are those cells?
DNA Overview: DNA (deoxyribonucleic acid) is the hereditary material in all known living organisms and many viruses. It carries genetic instructions for development, functioning, growth, and reproduction.
Cell Size: Typical human cells range from about 10 to 30 micrometers in diameter. However, sizes can vary significantly depending on the cell type.
What are genes? Use figure 1.6 to know that inherited DNA directs the development of an offspring of two parents.
Genes are segments of DNA that contain the instructions for the development, functioning, growth, and reproduction of organisms.
They are inherited from parents and play a crucial role in determining traits and characteristics of offspring.
Inherited DNA directs these processes, ensuring that genetic information is passed down through generations.
What are nucleotides and what are the 4 types? How does DNA encode information? Use the rat, tar, art analogy to explain this idea:
Nucleotides are the basic building blocks of nucleic acids, such as DNA and RNA. Each nucleotide consists of three components: a phosphate group, a sugar (deoxyribose in DNA), and a nitrogenous base.
The 4 types of nucleotides in DNA are:
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
DNA Encoding Information: DNA encodes information through the sequence of its nitrogenous bases. The analogy of "rat," "tar," and "art" illustrates how different arrangements of the same letters (nucleotides) can create distinct meanings (genes). Just as rearranging letters forms different words, varying nucleotide sequences produce different proteins and functions in organisms.
It is important for you to understand how the nucleotide sequence of a gene is used as a blueprint to make a specific protein. Know that proteins are molecular workhorses in a cell, and that each protein is a sequence of various amino acids folded in particular three-dimensional shapes. The sequence and shape determines protein function.
What is gene expression? Know crystallin, transcription, translation, mRNA:
Gene Expression is the process by which information from a gene is used to synthesize a functional gene product, typically proteins.
Crystallin: A type of protein found in the lens of the eye, crucial for maintaining transparency and refractive properties.
Transcription: The process of copying a segment of DNA into mRNA.
Translation: The process where ribosomes synthesize proteins using the mRNA sequence.
mRNA (messenger RNA): A type of RNA that carries genetic information from DNA to the ribosome, where proteins are synthesized.
How is the genetic code used to discern evolutionary relationships? How do we know that we are very closely related to Chimpanzees and only distantly related to mice and grasses?
The genetic code, composed of DNA sequences, is used to discern evolutionary relationships through comparative genomics. By analyzing similarities and differences in DNA sequences among species, scientists can construct phylogenetic trees that illustrate evolutionary lineages.
Humans and chimpanzees share approximately 98-99% of their DNA, indicating a recent common ancestor. In contrast, humans share about 85% of their DNA with mice and much less with grasses, reflecting more distant evolutionary relationships. These comparisons help establish the degree of relatedness among species.
What is the field of Genomics? What is a genome? How large is your genome? What is proteomics and what is a proteome? Learn, and please don’t memorize.
Definition: The process by which information from a gene is used to synthesize a functional gene product, typically proteins.
Key Components:
Crystallin: A type of protein found in the lens of the eye, important for transparency and refractive properties.
Transcription: The process of copying a segment of DNA into mRNA.
Translation: The process where ribosomes synthesize proteins using mRNA as a template.
mRNA: Messenger RNA, a type of RNA that conveys genetic information from DNA to the ribosome.
Field: The study of genomes, the complete set of DNA within an organism.
Genome Size: Human genome consists of approximately 3 billion base pairs.
Definition: The large-scale study of proteins, particularly their functions and structures.
Proteome: The entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time.16.
What are the three important research developments that have made genomic and proteomic approaches possible in recent decades? What is bioinformatics? Know the example I mentioned in lecture about the race to make a new vaccine.
Next-Generation Sequencing (NGS): Allows rapid sequencing of DNA, making genomic studies more efficient.
Mass Spectrometry: Enhances proteomic analysis by identifying and quantifying proteins in complex samples.
CRISPR-Cas9 Technology: Enables precise gene editing, facilitating functional genomics research.
Bioinformatics is the application of computer technology to manage and analyze biological data, particularly in genomics and proteomics.
Unknown.
How have humans affected the environment? Know those two paragraphs on climate change well with all those statistics and examples. (Starting with “Like other organisms, we humans interact….”). Approximately what % of CO2 released by fossil fuels remains in the atmosphere? How are organisms affected by this human-caused climate change? Specifically, how are Sceloporus lizards affected by this? Use fig. 1.11 and caption. What is extinction?
Approximately 50% of CO2 released by fossil fuels remains in the atmosphere.
Organisms are affected by climate change through habitat loss, altered food availability, and changing weather patterns.
Sceloporus lizards are particularly impacted as rising temperatures can affect their metabolism, reproduction, and survival rates. They may struggle to find suitable habitats as their preferred environments change.
Extinction is the permanent loss of a species, occurring when the last individual of that species dies, often due to environmental changes, habitat destruction, or human activities.
What are the three Domains? Know all examples and characteristics in that figure. Why don’t we classify protists under their own Kingdom?
Bacteria
Prokaryotic, unicellular organisms.
Peptidoglycan cell wall.
Diverse metabolic pathways.
Archaea
Prokaryotic, unicellular organisms.
Unique membrane lipids and no peptidoglycan.
Often extremophiles (e.g., thermophiles, halophiles).
Eukarya
Eukaryotic organisms (cells with a nucleus).
Includes kingdoms: Animalia, Plantae, Fungi, and Protista.
Complex cellular structures.
Protists are not classified under their own kingdom due to their diverse characteristics and evolutionary relationships, which make them more similar to multiple kingdoms rather than a distinct group.
Learn about Charles Darwin under that subtitle. What’s the famous book he wrote? What’s Descent with Modification? Why is it such an insightful phrase? Explain the two main points Darwin articulated in his book.
Famous Book: Darwin wrote "On the Origin of Species" in 1859.
Descent with Modification: This concept refers to the idea that species evolve over time, with changes passed down through generations.
Insightful Phrase: It highlights the process of evolution and the common ancestry of life forms.
Two Main Points:
Natural Selection: The mechanism by which individuals with favorable traits are more likely to survive and reproduce.
Variation: The existence of differences among individuals in a population, which is crucial for evolution.
Learn how birds show unity and diversity using figure 1.15. Be sure to know the caption in all figures.
What were Darwin’s three essential observations that helped him shape the theory of Natural Selection?
Darwin's three essential observations for the theory of Natural Selection are:
Variation: Individuals within a species show variation in traits, such as size, color, and shape.
Inheritance: Some of these variations are heritable and can be passed on to the next generation.
Differential Survival and Reproduction: Individuals with advantageous traits are more likely to survive and reproduce, leading to the gradual evolution of the species.
How is the human arm an example to illustrate the unity and diversity of life?
The human arm exemplifies unity and diversity in life through its anatomical structure and evolutionary significance.
Unity: All vertebrates share a similar bone structure (humerus, radius, ulna) due to common ancestry, illustrating the concept of homologous structures.
Diversity: Different species have adapted their limb structures for various functions (e.g., wings in birds, flippers in whales), showcasing how evolution shapes form and function based on environmental needs.
This duality highlights both the shared heritage and the adaptive variations among living organisms.
How can geographical separation split a species into two species? Use the example in my lecture on the squirrels of the Grand Canyon.
Geographical separation can lead to speciation through a process called allopatric speciation.
In the case of the Grand Canyon squirrels, the canyon acts as a barrier, dividing a single squirrel population into two isolated groups. Over time, these groups experience different environmental pressures and genetic drift, leading to adaptations that make them distinct. Eventually, reproductive isolation occurs, resulting in the emergence of two separate species.
How can the Tree of Life be used to illustrate that all life descended from unicellular prokaryotes?
The Tree of Life illustrates the evolutionary relationships among all living organisms, showing that they share a common ancestor. By tracing back the branches, we can see that all complex life forms, including plants and animals, diverged from unicellular prokaryotes (like bacteria). This representation highlights the concept of common descent, demonstrating how diverse life evolved from simple, single-celled organisms over billions of years through processes like natural selection and genetic variation.
What is science? What is inquiry?
Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe. It involves observation, experimentation, and analysis.
Inquiry is the process of seeking information, understanding, or knowledge through questioning, investigation, and exploration. It often involves formulating hypotheses and conducting experiments to gather evidence.
The enterprise of science begins with what? What are data? What are the two types of data? Give examples from Jane Goodall’s work on Chimpanzees.
The enterprise of science begins with observation and questioning.
Data are facts and statistics collected for analysis.
The two types of data are:
Qualitative Data: Descriptive information (e.g., behaviors of chimpanzees, such as grooming or social interactions).
Quantitative Data: Numerical information (e.g., the number of chimpanzees in a group or the frequency of specific behaviors).
Jane Goodall's work includes observing social behaviors (qualitative) and counting individuals in her study groups (quantitative).
What is a hypothesis? What kind of reasoning is involved when you form a hypothesis? For a hypothesis to be valuable it has to be ______.
A hypothesis is a testable statement or prediction about the relationship between variables.
The reasoning involved in forming a hypothesis is typically inductive reasoning, where observations lead to generalizations.
For a hypothesis to be valuable, it has to be falsifiable, meaning it can be proven wrong through experimentation or observation.
How can you test a hypothesis? (two ways).
Conduct experiments: Manipulate variables in a controlled environment to observe outcomes.
Perform observational studies: Collect data in natural settings to identify patterns or correlations.
What is a theory? What would you say to a student who rejects evolution as “just a theory”?
A theory in science is a well-substantiated explanation of an aspect of the natural world, based on a body of evidence.
What are the 4 ways a scientific theory are different from a hypothesis?
Definition:
Hypothesis: A testable prediction or educated guess about the relationship between variables.
Theory: A well-substantiated explanation of an aspect of the natural world, based on a body of evidence.
Evidence:
Hypothesis: Requires testing and experimentation to gather evidence.
Theory: Supported by extensive evidence and has withstood repeated testing.
Scope:
Hypothesis: Narrow in scope, often specific to a particular experiment.
Theory: Broad in scope, explaining a wide range of phenomena.
Status:
Hypothesis: Considered provisional and subject to rejection or modification.
Theory: Generally accepted within the scientific community until disproven or revised.
Know the 3 key concepts
Learn the overview using fig. 19.1 What does this moth and its Lepidopteran relatives teach us about the unity and diversity of life?
Know the 3 key observation about life we can derive from this example.
What are the 2 ways we can define evolution? (One: Descent with modification, Two: change in genetic composition of a population from generation to generation).
Concept 19.1. The Darwinian revolution challenged traditional views of a young earth inhabited by unchanging species
Know about Aristotle’s Scala Naturae and the ladder of life.
Learn the role played by fossils in changing of ideas over time. Know figure 19.3. What is paleontology?
Know Lamarck’s hypothesis. When did he publish it? Know the principle of use and disuse and inheritance of acquired characteristics. How did he use the giraffe to explain these? Was he right? Why does he deserve rightful recognition? Know figure 19.4.
Concept 19.2. Descent with modification by natural selection explains adaptations of organisms and the unity and diversity of life
Know all about the voyage of the Beagle. Use figure 19.5. Where and when did they sail? Where are the Galapagos Islands?
Know the para under Darwin’s focus on Adaptation. Know fig. 19.6.
Why was he reluctant to publish his findings? Who was Alfred Russell Wallace? Where were his travels? Know the para starting with “In June 1858…” that explains their complicated relationship. Use figure 19.7.
Be sure to watch the The Origin of Species: The Making of a Theory video. It is an excellent summary of what these two great naturalists accomplished and found out. Please use the transcript PDF available in the HHMI website (link in Blackboard) and study that also after watching the film. Be sure to understand the location and significance of the Wallace’s Line. What kind of mammals predominate east of this line? West of this line?
Ideas from The Origin of Species
We went over the first two paragraphs including figure 19.8. Know these and explain the tree of life as Darwin did. See a real life example in fig. 19.9.
Artificial Selection, Natural Selection, and Adaptation
Use fig. 19.10 to articulate how Darwin used artificial selection as an analogy for natural selection.
Know the two observations and two inferences. Use figs. 19.11 and 19.12 and their captions.
Key Features of Natural Selection
Know the three main ideas (bulleted points) using fig. 19.13 and its caption.
Know the three key points about Natural Selection under fig 19.13. Can individuals evolve? In a given heritable trait, if all individuals have it identically, can evolution occur? Why or why not? Can a trait be an asset at some time or place and then become a liability?
Concept 19.3. Evolution is supported by an overwhelming amount of scientific evidence
Read the first two paras. What 4 types of data do we cover here that document evolution and illuminate how it occurs?
Direct observations of evolutionary change
Learn in depth the soapberry bug example and the field study to test the hypothesis. Can selection for beak length occur only one way? Why or why not? Be sure to thoroughly know the graph under Results. How did they measure beak lengths before introductions? How rapid was this evolutionary change in c. Florida?
Also know in depth the important issue of bacterial resistance to antibiotics. What are MRSA and USA300? Know figure 19.17. What are the nonblue areas and what do they signify? How big is the genome?
Know the story of how it began in 1943 and how it progressed (first 3 paras)
Read the para that starts with “The S. aureus and soapberry bug examples……” to learn the three key points about natural selection. These are points we have covered before and this helps reinforcing those important points. Remember, natural selection cannot cause variations; and individuals don’t evolve, populations do; and a favorable trait today or in some place may not be so tomorrow or in another place.
Homology
What is homology? Use fig. 19.16 for an excellent example of anatomical homology; and fig. 19.17 for anatomical homology. Be sure to know the captions.
What are vestigial structures? Know the examples from snakes and fishes.
A Different Cause of Resemblance: Convergent Evolution
What is it? Is it common? Use fig. 19.18. What is the opposite of homologous? So the “wings” (patagium) of the sugar glider and flying squirrel are said to be analogous organs.
The Fossil Record
Know the stickleback example and what it means.
Use fig. 19.19 to know how ankle bones provide insights into cetacean ancestry. Be sure to know the caption well.
Also use fig. 19.20 to know how the ancestors of whales started as 4-legged terrestrial (=land-based) mammals and them progressively evolved the streamlined shape that cetaceans have for movement in water. Know how the highlighted organisms adapted by modifying their hindlimbs using the color coded bones.
Biogeography
Know continental drift, Pangaea, when they occurred. Know the Equus example to learn how we can make predictions of where fossils of different groups of organisms might be found.
What is endemic? Why do islands have a lot of endemics? Why do islands like the Galapagos have clusters of closely related species? Why do two islands with similar environments in distant parts of the world (like Hawaii and Galapagos) don’t share similar species, but have species more allied to nearest mainland?
Is this JUST A THEORY?
How do scientists use this word compared to popular usage?
Can predation result in natural selection for color patterns in guppies? This is an important section. Learn it well in its entirety, including the figure and experimental design and the graph. How many generations and months passed for this change to occur? Where did this study take place? What are the two predators? Etc etc.
