Geo Sci Study Guide PDF

What are the key, high-level components of the Central Dogma? How far down can you drill into each of those components and how well can you describe what is going on? What are the implications for evolution? \[NOTE: this question encompasses pretty much everything that follows in this section!\] -...

What are the key, high-level components of the Central Dogma? How far down can you drill into each of those components and how well can you describe what is going on? What are the implications for evolution? \[NOTE: this question encompasses pretty much everything that follows in this section!\] - DNA Replication: Description: The process by which DNA makes a copy of itself, ensuring that genetic information is passed on during cell division. Key enzymes involved include helicase, DNA polymerase, and ligase. Details: DNA is unwound at the replication fork, RNA primers are synthesized, and new strands are formed by adding complementary nucleotides to the template strands. Errors can lead to mutations, which may have evolutionary implications. - Transcription: Description: The process of converting DNA into messenger RNA (mRNA). Details: RNA polymerase binds to a gene\'s promoter region, unwinds the DNA, and synthesizes an mRNA strand by adding complementary RNA nucleotides. Post-transcriptional modifications, such as splicing, add further complexity by removing introns and adding a 5\' cap and poly-A tail. - Translation: Description: The process where mRNA is translated into a protein. Details: Ribosomes read the mRNA in codons (three-nucleotide sequences), and transfer RNA (tRNA) brings the corresponding amino acids. The ribosome links these amino acids together to form a polypeptide chain, which folds into a functional protein. - What are some of the important properties of the DNA molecule that allow it to store and convey information? - A(Adenine), C(Cytosine), T(Thymine), G(Guanine) are all important in both store and convey information. What are the nucleobases (aka "bases") in DNA and how do they interact with one another? 1. Adenine 2. Guanine 3. Cytosine 4. Thymine - Adenine (A) pairs with Thymine (T) through two hydrogen bonds. - Cytosine (C) pairs with Guanine (G) through three hydrogen bonds. - Nucleobases interact with one another through hydrogen bonds, ultimately forming base pairs. What is involved in DNA replication and what is the expected outcome of that process? - DNA replication involves unwinding the double helix, synthesizing RNA primers, and elongating new DNA strands using DNA polymerase. - It produces two identical DNA molecules, each consisting of one original strand and one newly synthesized strand (semiconservative replication). - This process ensures genetic consistency and prepares the cell for division, allowing for accurate distribution of genetic material to daughter cells. How many base pairs are in our genome (i.e., single copy of our DNA)? Does the size of the genome convey anything important about the properties or complexities of organisms? - The human genome contains approximately 3 billion base pairs. However, the size of the genome does not directly correlate with the complexity or properties of the organism, as complexity can arise from factors like gene regulation and non-coding DNA.\" What are proteins and what roles do they play in life? - Proteins are structures formed by amino acids. 5. Provide Structure. Structural proteins are a type of protein responsible for cell shape and providing support to major structures, such as hair, skin, and bones 6. Regulate Body Processes. Proteins regulate many processes within the body. 7. Transport Materials What are amino acids?  - Amino acids are the molecules that combine to form proteins. Amino acids and proteins the building blocks for life. How is RNA similar to and different from DNA? What is mRNA, where does it come from, and what does it do? Are there other types of RNA? - Similar: RNA and DNA are similar in the sense they are both nucleic acids made up of nucleotides Different: - DNA is a double helix, while RNA is single-stranded - DNA contains deoxyribose sugar, while RNA contains ribose sugar.  - Both share adenine (A), guanine (G), and cytosine (C), but DNA has thymine (T) while RNA has uracil (U).  MRNA is a type of RNA that is responsible for carrying genetic code from DNA to Ribosomes to conduct protein synthesis Other types: - tRNA: Carry amino acids to the ribosomes during protein synthesis - rRNA: Form the core of the cells ribosomes What are ribosomes and tRNA and how do they interact to build a protein? - Ribosomes: Cellular structures that synthesize proteins by linking amino acids together. - tRNA is responsible for carrying amino acids to the ribosomes during protein synthesis. - During protein synthesis, tRNA transfers amino acids to the ribosome, where they are matched to the corresponding codon on a messenger RNA (mRNA) strand. This process allows the ribosome to link the amino acids together, forming a protein chain. What is a codon? In what ways is redundancy built into the genetic code? What are some implications of that redundancy? - A codon is a sequence of three nucleotides in either DNA or RNA that codes for a specific amino acid. Genetic code can be deemed redundant because multiple codons can code for the same amino acid. Implications of redundancy can build protection against mutations, allowing for errors within the DNA sequence without altering the resulting protein structure. What are some of the mechanisms that lead to changes in the genome? - The primary mechanisms that make changes in the genome are mutation (errors during DNA replication), genetic recombination (rearrangement of genetic material during cell division), and transposable elements (mobile DNA sequences that can insert themselves into the genome), which can result in alterations like deletions, insertions, inversions, and duplications of DNA segments within the genome What is a "silent mutation?" - Point mutations that cause no change in amino acid identity are called silent mutations What is a "gene"? - Genes are segments of DNA that act as the base unit for heredity, with =in genes contains instructions for different traits like eye color and height. Are all portions of an mRNA turned into protein? - No, only the coding region of exons is turned into proteins from being turned into amino acids. About what percent of the human genome actually codes for proteins? What are the implications for/causes of that? - Only about 1-2% of the human genome actually codes for proteins. The vast majority that are noncoding regions infer that with increased complexity and can impact health, as variations in these regions may influence gene expression and contribute to genetic disorders. What is reverse transcription and how do retroviruses work? - Reverse transcription happens when information is transferred from RNA back to DNA. This can happen when being infected by HIV. - Retrovirus's work by transcribing their RNA back into DNA. Which is then inserted into the host genome. Where host cells treat the virus as one of their own. What is the significance of the homology that is represented by the Central Dogma? How does that all relate to Darwin's ideas? [Mendelian Genetics] - How did Gregor Mendel go about determining the rules for what would come to be known as "Mendelian genetics?" What are those rules? - Gregor Mendel determined his rules for mendilian genetics through his experiments with pea plants. He came up with two main principles. 1. Principle of segregation - Each parent contributes one randomly chosen allele from each gene to each offspring 2. Principle of independent assortment - Allele pairs (genes) behave independently of all other allele pairs - Homozygotes have two copies of the same allele (dominant or recessive) for a gene; heterozygotes have a dominant and recessive copy - What is the difference between a phenotype and a genotype? Which is relevant to natural selection and why? - Phenotype refers to the observable physical traits of an organism, while genotype refers to its genetic makeup at the molecular level. The phenotype is relevant to natural selection because it is the traits that influence survival and reproduction. - Can you predict the outcome of reproduction for any Mendelian case? For example, what are all of the predictions if you cross two individuals that are heterozygous for a Mendelian trait? - Yes you can predict the outcome of reproduction for anh mendelian case. When crossing two heterozygous individuals (Aa), the genotypic ratio among the offspring is 1 AA, 2 Aa, and 1 aa, - There are many examples of non-Mendelian behavior. Can you list several examples and explain them? - **Incomplete Dominance**: In this scenario, neither allele is completely dominant over the other, resulting in a phenotype that is a blend of both traits. For example, in snapdragons, crossing a red flower (RR) with a white flower (WW) produces pink flowers (RW), illustrating that the phenotype is an intermediate expression of the two alleles. - **Co-dominance**: In co-dominance, both alleles in a heterozygous individual are fully expressed, resulting in a phenotype that shows both traits simultaneously. A classic example is seen in blood types: individuals with the genotype IAIB express both A and B antigens on their red blood cells, resulting in type AB blood. - **Multiple Alleles**: Some genes have more than two alleles in a population, which can lead to a range of phenotypes. The ABO blood group system is a prime example, where the three alleles (IA, IB, and i) result in four possible blood types (A, B, AB, and O), showcasing the complexity of inheritance beyond simple dominant/recessive relationships. - **Ecophenotypic Variation**: This refers to phenotypic variations that arise from environmental influences rather than genetic differences. For example, the growth form of plants can change based on environmental factors like light and water availability, leading to different appearances even among genetically identical individuals - What is the importance of identical twin studies and what do they demonstrate? - Identical twin studies are important for demonstrating how different environments can influence individual appearance and phenotype. By comparing identical twins raised in different environments, researchers can highlight the effects of genetics versus environmental factors on traits - What are chromosomes and how do they relate to Mendelian genetics? - Chromosomes are structures made of DNA and proteins that carry genetic information. In Mendelian genetics, chromosomes play a key role because they contain the genes that determine inherited traits from the parents. **Oct. 4: Week 5** [Natural Selection] - What is required in order for natural selection to occur? Do these requirements occur in nature? - [Variability:] Offspring are not all identical to their parents as well as not identical to the rest of the individuals within the population - [Heritability]: Traits are passed on from parents to offspring - [Differential reproductive success]: individuals within a population that have more advantageous traits produce more offspring to the next generation then others. - In what sense, if any, is natural selection, or a natural selection-like process, "creative?" - Natural selection can be creative in the sense that it creates high levels of diversity and complexity to biological systems. - A common pattern when selection first occurs is for the population to change rapidly and then more slowly as time passes. Why might this be? - Initially, rapid changes occur in a population due to abundant genetic variation and strong selective pressures favoring certain traits. As these traits become prevalent and the population adapts, the rate of change slows down due to diminishing returns, genetic constraints, and stabilizing selection. - What is "fitness" in the biological and natural selection sense of the word? - fitness is the relative ability to reproduce and contribute offspring to the next generation - What are the types of selection, or selection regimes, and how do they affect populations? - [Directional Selection:] - Selection of one end of the distribution of traits - Causes directional change in the population morphology - No change in original variability in the population - Ex. This type occurs when one extreme phenotype is favored, leading to a shift in the population\'s traits. An example is the increasing size of horses over time, which favored larger individuals for their advantages in survival and reproduction. - [Stabilizing selection] - Selection against the extremes (and members) within a population - May cause decreased variability in a population if rate of introduction of new variants is low relative to strength of stabilizing selection - Ex. This occurs when intermediate phenotypes are favored, reducing variation in a trait. For example, human birth weights show stabilizing selection, as babies that are too small or too large have lower survival rates. - [Disruptive Selection] - Selections for the extremes in a population - Results in divergence away from existing mode - Usually results in an increase in the variability of a population - Ex. In certain butterfly species, individuals with either very bright or very dull coloration are favored. Bright colors may attract mates, while dull colors provide better camouflage from predators, while those with intermediate colors might not be effectively camouflaged or appealing. - Drift: No selection - Does natural selection always have to result in change over time? Why or why not? - No because natural selection can favor intermediate traits, which ultimatley leads to stabilizing selection, especially in stable environments causing little to no change. - What is the "adaptive landscape" and how do populations respond to it? - The \"adaptive landscape\" is a model that represents how different phenotypes (or genotypes) correspond to fitness levels in a given environment with peaks and valleys. Populations respond to this landscape by evolving toward higher fitness peaks through natural selection, migration, or mutation, which can lead to changes in traits that improve survival and reproduction in a enviorment - We previously discussed homologous, analogous, and vestigial structures? How are each of these explained in light of Darwin's hypothesis? - Homologous Structures: These are body parts that share a common ancestry but may have different functions, like the forelimbs of mammals. Darwin explained these as evidence of divergent evolution, showing how species adapt differently from a shared ancestor. - Analogous Structures: These perform similar functions but do not share a common evolutionary origin, such as wings in birds and insects. Darwin viewed these as results of convergent evolution, where unrelated species adapt similarly to similar environments. - Vestigial Structures: These are remnants of features that served a function in an ancestor, like the human appendix. Darwin interpreted these as evidence of evolution, indicating that certain traits can diminish in importance as species adapt. - How does Darwin's mechanism explain changes in fossils over time?  - Darwin's mechanism of natural selection explains changes in fossils over time by showing that as species adapt to their environments, new traits emerge, leading to the gradual evolution of different forms. - Darwin famously drew a diagram to illustrate what he thought was the outcome of natural selection and evolution. What are the key features of that diagram and why was it so impactful?   - What were some of the gaping holes in Darwin's understanding of natural selection (and evolution generally)? - Darwin didn't have a proper understanding of genetics and heritability, which created a grey area in how traits were inherited and how variability worked. [Checks on Population Growth] - Why must there be checks on population growth in nature? - if a population grows unchecked, it will eventually exceed the available resources in its environment, leading to competition for food, water, and shelter, which can result in widespread starvation, disease, and ultimately, a population crash - What are density dependent and density independent checks on population? Can you give some examples of each and explain them? - Density independent\" refers to factors that affect a population regardless of its size or density, while \"density dependent\" factors influence a population based on how crowded it is - Independent: ex. Natural Disaster - Dependent: ex.disease spread given how crowded it is, insufficient resources. - What are food webs and why might they matter to population sizes? - Food webs are complex interactions both positive and negative that contribute to growth rate. They matter to population sizes because without these food webs, we could see organisms go unchecked and grow exponentially, leding to for example overpopulation and resource depletion. - What is "logistic growth" and how is it achieved by natural populations? - Logistic growth is the idea that all living organisms if gone unchecked, have the potential to reproduce rapidly but to rapidly to become sustainable at that size - Factors such as resource competition, predation, and disease regulate this process, preventing overpopulation and maintaining ecological balance. - What is a "carrying capacity" and what might determine it? Carrying capacity is the maximum amount of organisms that can be sustainably supported by the environment. When organisms exceed this capacity, we can see resource depletion as well as a decrease in populations from the negative extraneities of exceeding the carrying capacity. -ex. Deer in Forests: In a forested area, the carrying capacity for deer is determined by food availability, shelter, and water. If deer populations exceed this capacity, overgrazing can occur, leading to habitat degradation and a subsequent decline in the deer population. **Sept 27: Week 4** [Darwin's Origin of Species: Struggle for Existence] - The third chapter of the Origin of Species is titled "Struggle for Existence" (we are reading this in discussion sections). What fundamental fact about all organisms is central to Darwin's assertion about a "struggle"? What led Darwin to the realization? - We covered some math and used a simple model to describe the inherent potential of populations to grow. Can you qualitatively describe that model and identify its basic mathematical underpinnings? - What are some important properties of a population? - What are the parameters of a population that determine its characteristic growth rate? Does that growth rate always have to be positive? Why or why not? - Does the term "exponential growth" (aka "geometric growth") apply to the human population? How do we know either way? [Darwin's Origin of Species: Variation in Nature] - The second chapter of the Origin of Species is titled "Variation under Nature." Give some examples of how organisms vary in nature and describe why that is relevant to selection. [Darwin's Origin of Species: Domestic Variation] - The first chapter of the Origin of Species is titled "Variation under Domestication." What did Darwin seek to demonstrate in this chapter? - What is "artificial selection" and how is or is it not different from "natural selection?" - Domestic pigeons figured prominently in Darwin's first chapter. What are some general properties of domestic pigeons and how do they relate to the argument for the power of selection? - Why did Darwin try to distinguish between methodical, purposeful selection and unconscious, accidental selection when considering domestic breeding?  - What is allometric and isometric growth in organisms and what is the potential significance of this difference to breeders? - What is heterochrony? How is it relevant to the possible effects of selection? - What are some possible reasons for the differences in variability that exist between domestic dogs and cats? - What is meant by "heritability?" - What properties of organisms are most important to domestic breeders and why? [Charles Darwin and observations leading to the Origin of Species] - What were some key aspects of the "state of knowledge" surrounding geology and biology around 1850, just before Darwin published the Origin of Species? - How did Darwin explain coral reef atolls and what is the relationship, if any, between their mode of formation and his ideas about the origin of species? - What were some of the key observations made during the voyage of the Beagle that contributed to Darwin's ideas about the origin of species? - Why were the properties of organisms on islands, like the Galapagos, so important to the development of Darwin's ideas? - Who was Alfred Russel Wallace and why was he important to the eventual publication of the idea of natural selection? **Sept 20: Week 3** [Faunal Succession] - How and why did William Smith go about studying fossils? - William smith started studying fossils because as a foreman, and often difgging canals, he wanted to study them to understand how long it would take him approximetly to dig through certan areas of rock. - What was the significance of the first geologic map, which was made by William Smith? - William smiths map marked a large scale prediction as to where certain strata were distributed. And what rock types specifically were distributed. He also created geological mapping with this creation of his. - What is "faunal succession" and how is it used to understand the rock record? - Faunal succession is an aging tool in which newer rock types succeed older rock types. It is useful for identifying the ages of rocks deposited in layers and provides geologists with a general timeline of geological events and record. As well as how earth has changed over the years. - What is biostratigraphy? - correlation (identification of similar age) of strata and determination of relative ages based on the INDEX FOSSILS that those strata contain. - How was the geological timescale initially constructed and what are the two types of dating that can be applied to the rock record? - Relative Dating: This method ranks events and rock layers in relation to one another, allowing geologists to determine the sequence of events without assigning specific ages. - Numerical Dating: Also known as absolute dating, this method provides a specific age or date for a rock or event in years. - What are some of the large-scale trends (i.e., changes over time) that are observed in the fossil/rock records? - Mass extinction - Climate Change - Evolution - Changes in dominant organisms - Changes in the diversity of life [Extinction and Early Idea of Evolution] - What were some of the conceptual problems posed by the possibility of extinction? - Th possibility of extinction was contradicted by the bible, and the bible held a lot more weight. - Violated principle of Plentitude (Nature is as complete as it gets) - What is comparative anatomy and how is it useful in the study of fossils and living things? - Comparative anatomy is the study of similarity and differences between the morphology of living and fossilized organisms. - Comparative anatomy identifies key morphological traits of organisms that are used to classify organisms together. - What types of fossils did Cuvier study and how did they lead him to the conclusion that extinction is a real phenomenon? - Cuvier studied the fossils of an animal called the "Ohio Animal", he proved that fossils from mammoths were distinctly different than any living elephant species. Proving that this animal is no longer living, proving that it went extinct. - How did Cuvier explain the observation that fossils change between successive strata? - Cuvier found that the older rock strata you find, the more and more these fossilized organisms do not resemble modern living organisms. And that newer organisms would be found in successive rock strata. - How did Lamarck explain the observation that fossils change between successive strata? - Can you describe Lamarck's concept for how and why organisms change over time? - What are homologous, analogous, and vestigial structures in organisms, can you name some examples? - **Homologous structures** arise from a common ancestor and may serve different functions (e.g., the forelimbs of mammals, birds, and whales). - **Analogous structures** serve similar functions but do not share a common ancestor (e.g., wings of b ats and insects). - Vestigial -- Structures/Organs that once served a purpose, but over time through evolution still exist but serve no purpose. Ex apenex - Why was the development of an individual animal from an egg to an adult referred to as "evolution?" - The development of an individual animal from an egg to adulthood shows how organisms undergo structural and biological changes over time. As we grow, our arms and brains evolve, and various parts of our bodies adapt to serve different functions in adulthood. Thus we are evolving in that time. - What are some features of developing animal embryos that suggest that changes have or can occur over time? [Discovery of Deep Time (cont)] - What are cross cutting and enclosing relationships? - Can you work out the relative order of geological events when presented with a diagram showing a cross-section of the Earth, like this? **Sept 13: Week 2** [Discovery of Deep Time] - What are Steno's principles of stratigraphy? - [Principle of original lateral continuity] - - strata were originally deposited continuously unless interrupted by solid object; gaps in the same strata indicate material has been removed after their formation - [Principle of original horizontality] - strata are deposited on Earth's surface horizontally, or nearly so; departures indicate strata have been moved after they formed - [Principle of superposition] - strata are arranged in a temporal order, with oldest at bottom, buried progressively, with the youngest at top Principle of superposition - What are "strata" and how do they form? 1. **Compaction**: Overlying weight compresses layers. 2. **Cementation**: Minerals bind particles into rock. 3. **Uplift and Erosion**: Forces expose and erode layers. 4. **Burial**: New layers cover older ones - How did Steno's work challenge the notion that Noah's flood washed fossils onto mountains? - What is uniformitarianism? What types of uniformity apply in this world view? - Uniformitarianism is a process tha tis used to today to undertnd processes of the past. For example waves in the water today making ripples in the sand, and how that relates to fossils showing similar characteristics of the ripples. - What is the sedimentary cycle? - The sedimentary cycle refers to the processes involved in the formation, transport, deposition, and lithification of sedimentary rocks - What are the temporal implications of "angular unconformities?" - Angular unconformities provide important insights into Earth\'s past, revealing geological events that disrupted sedimentation and caused erosion. They indicate significant time gaps between rock layers, helping geologists understand the history of tectonic activity and changes in the environment. - What led Hutton to conclude that the Earth must be very old? [Great Chain of Being] - What is the old Scala Naturae and how does it differ from the Linnaean hierarchy? - Scala Naturae focuses on fixed relationships between entities that cannot be changed or reclassified, while the Linnaean hierarchy classifies organisms into groups based on shared characteristics and can be adapted and rearranged as evolution occurs. - What are the names of the ranks of the Linnaean hierarchy and their order? 1. Kingdom 2. Phylum 3. Class 4. Order 5. Family 6. Genus 7. Species - What was the most controversial aspect of Linnaeus' classification scheme? - That it was all from divine order from God and created entities were fixed in nature. While some organisms where deemed superior then others. - What is a species? - According to lineages, species where specially created entities that where fxed into nature as the original forms from the Garden of Eden. - What observations pose problems for the definition of a species and ultimately caused Linnaeus to abandon the notion that species are "fixed in nature"? - What is a cladogram? - A diagram of hierarchy based on similarity. Ex like a phylogeny tree - What are the three domains of life and what are some of the properties of those domains? 8. Eukarya -- Cells with a nuclease, such as plants and animals, Eukaryotes 9. Archaea -- Single cell organisms with no nucleus, Prokaryotes, different genes than bacteria for reading out and managing their DNA 10. Bacteria -- Single cell organisms with no nucleus, Prokaryotes, [Finding the Meaning of Fossils] - Why was the organic interpretation of fossils not obvious in the early Renaissance? - The organic interpretation of fossils was not obviousin the early Renaissance due to prevailing religious beliefs and a limited scientific understanding. Many fossils were misinterpreted as curiosities rather than remnants of ancient life, and the lack of comparative anatomy further hindered this understanding. - What were some of the conceptual problems posed by fossil objects? 1. How did they become part of the rock? 2. Are fossils just like living orgasms or were they once living orgasms at one point. - How did Nicholas Steno conclusively demonstrate that some fossil objects are the remains of once living things? - Steno conclusively demonstrated that some fossils were remains of once living things through studying patterns of growth as well as relizing that "tongue stones" from sharks where actually their teeth which where often found embedded in rocks. - What are fossils in the modern sense of the word? Include the three types of fossils in your answer. - Fossils are them remains of once living organisms preserved through the bial of rock and other minerals. 3. Body Fossils 4. Trace Fossils -- ex a footprint 5. Molecular Fossils -- Chemical compounds - What are some properties of organisms that make them more likely to be preserved as fossils? - Very hard parts -- such as bones, shells , and teeth since they are tougher and more resistant to decay - Larger parts - How was the common occurrence of fossils of ocean animals in the rocks of mountains first explained? - It was first explained by a flood, where rainfall was so heavy and so intense that organisms from the oceans were washed up/crawled on the mountain and left their when the water receded, known as "Noah's Flood". - What potential role did top-down, religiously oriented explanations for fossil objects play in the development of science? **Sept 6: Week 1** [Emergence of science as an approach to understanding our place in the universe] - What are some of the fundamental questions about our physical world/universe that religions attempt to answer? - Origins: Where do we come from? What is the creation story? - Purpose: What is the meaning of life? Why are we here? - Morality: What is right and wrong? How should we live? - Afterlife: What happens after we die? Is there life beyond this one? - Nature of the Universe: What is the nature of reality? Is there a higher power or divine force? - What were some of the predictions of the Abrahamic biblical account of the world and how did religion help motivate the systematic study of nature? - The Abrahamic religions, particularly through texts like the Bible, provided narratives about creation, humanity\'s role, and the moral order of the universe. - How did Galileo's approach to understanding the world differ from Bishop Ussher's? - Galileo's approach to understand the world came through observation and conducting experiments, and his advocation for the use of the scientific method. While Bishop Ushers came from more textual interparticle from the bible. Like when made the assumption that earth was x amount yers old all based from the bible. - What observations did Galileo make that decentralized Earth as the vessel of creation? - Galileo realized that Jupiter had moons orbiting around it, proving that the long-believed idea that the earth was the center of the universe was actually not true. - What distinguishes a scientific theory? - Testability: It can be tested and potentially falsified through experimentation or observation. - Predictive Power: It can make predictions about future observations or experiments. - Empirical Support: It is based on evidence gathered through systematic observation and experimentation. - Consistency: It should be consistent with existing scientific knowledge and theories. - Revisability: It can be revised or replaced in light of new evidence.