BIOL005B Study Guide PDF

BIOL005B Study Guide Lecture 1: The Human Brain and Consciousness Be familiar with the course structure, expectations, assignments, syllabus, etc Review the reading and understand “the hard problem of consciousness” ​ While neural correlates of consciousness suggest that the parts and function...

BIOL005B Study Guide Lecture 1: The Human Brain and Consciousness Be familiar with the course structure, expectations, assignments, syllabus, etc Review the reading and understand “the hard problem of consciousness” ​ While neural correlates of consciousness suggest that the parts and functions of a brain produce the informational contents of mind, they don’t explain our subjective experiences of perception What we mean by “emergent feature” (use consciousness as an example as discussed) ​ properties that arise from the interactions of multiple components within a system, but are not properties of the individual components themselves ​ Consciousness is an emergent feature because we cannot prove where consciousness comes from. It appears to arise from complex interactions between neurons, but it cannot be attributed to a single neuron alone because it emerges from a system of neurons. ​ Properties are not predictable based on the behavior of an individual component The difference between “system i” and “system ii” and their “jobs” in information processing ​ System I: fast, automatic, and operate intuitively without any conscious effort. It's your brain's default mode for quick, reactive thinking. ​ System II: slow, effortful, and involves conscious thought. It is activated when more complex and novel problems require logical reasoning. ○​ Has to be activated, like when solving a math problem. Definition of learning and memory and their relationship to each other ​ Learning: the process by which new knowledge is acquired ​ Memory: the process by which new knowledge is encoded, consolidated, stored, and retrieved ​ Learning is how we gain information and memory is how we retain and recall that information. ​ Short term memory is retained briefly, but released if irrelevant. New information that is learned must be encoded by association with existing knowledge. Consolidation stabilizes newly encoded information for long term storage. Retrieval assembles long term memories into working memory. Four steps involved in information processing (and the associated vocabulary) – like “short” or “long-term” memory, etc ​ Short term memory is retained briefly, but released if irrelevant. New information that is learned must be encoded by association with existing knowledge. Consolidation  stabilizes newly encoded information for long term storage. Retrieval assembles long term memories into working memory. Methods of promoting long-term memory storage ​ Immediate reinforcement ​ Short study sessions over longer periods of time ​ Make the information relevant to you (emotion) Broadly, how nervous systems allow for response to environmental stimuli (three steps) 1.​ Sensory input 2.​ Integration 3.​ Motor input Understand electrochemical gradients and how they can be used to store energy (including terms like voltage and membrane potential) ​ Electrochemical gradients: the distribution of electrical charges and concentration particles is not the same across two areas, which creates a membrane potential ○​ Cells harness the energy stored in electrochemical gradients to power various processes, such as the electron transport chain ​ Voltage: the measure of potential energy generated by separate charges ​ Membrane potential: voltage in a cell *in order for diffusion to occur there has to be a difference in concentration Start looking at the neuron Lecture 2: What is an Organism, Anyway? The basic structure of a neuron and broadly how signals are transmitted between them (including new vocabulary) ​ Dendrites: receive information from other neurons ​ Presynaptic cell: fires neurotransmitters (signals) ​ Axon: portion of neuron that carries impulses away from cell body to other cells ​ Postsynaptic cell: receives neurotransmitter (signals) ​ Synaptic Terminals: releases chemical messengers to transmit information between neurons ​ Electrical impulses travel down the length of the axon to the next neuron and continue travelling down each axon in order for signalling to occur Each step in generating an action potential and what facilitates the movement of ions Threshold = -55mv  1.​ Resting state is when the gated Na+ and K+ channels are closed. The inside of the cell is negative because it is polarized. 2.​ Depolarization occurs when a stimulus opens some sodium channels, allowing Na+ to flow through those channels and depolarizes the membrane. If the depolarization reaches the threshold voltage, it triggers an action potential. 3.​ In the rising phase of the action potential, depolarization opens most sodium channels while the potassium channels ramian closed. Na+ makes the inside of the membrane more positive compared to the outside. 4.​ In the falling phase of the action potential, most sodium channels become inactivated which blocks Na+ inflow. Most potassium channels open, which permits K+ outflow and makes the inside of the cell negative again. 5.​ Undershoot occurs when the sodium channels close, but some potassium channels remain open. As potassium channels close and the sodium channels become unblocked, the membrane returns to a resting state. Articulate the concept of “emergence” as it applies to living organisms ​ When new properties emerge at different levels of scale based on the random interactions occurring at lower levels ​ Ex. Atmospheric disturbances arise becoming hurricanes. Birds becoming flocks. People inhabiting a place and a neighborhood forming. ​ New properties and behaviors emerge with no directing and no one able to foresee the new characteristics from knowledge of the constituents alone What we mean by “levels of biological hierarchy” ​ You start with something small, and work your way up to a bigger phenomenon Elementary particles interact to form subatomic particles ↳ Subatomic particles interact to form atoms ↳ Atoms interact to form molecules ​ ↳ Molecules interact to form macromolecules ​ ​ ↳ Macromolecules interact to form cells ​ ​ ​ ↳ Cells interact to form tissues ​ ​ ​ ​ ↳ Tissues interact to form organs ​ ​ ​ ​ ​ ↳ Organs interact to form organ systems How biologists define life (all seven processes) 1.​ Homeostasis: regulation of internal state 2.​ Organization: one or more cells 3.​ Metabolism: energy capture 4.​ Growth: produce new parts  5.​ Adaptation: change in traits of populations over time (long-term) 6.​ Response to stimuli: individuals response to environment (short term) 7.​ Reproduction: make offspring Articulate the “thermodynamics perspective” of life ​ Taking energy in order to power a process, use of energy in a stepwise fashion ​ Ordered chemical reactions that keep us constantly from equilibrium with our surrounding environment Start considering all the reasons why life is tricky to define – more soon ​ There are multiple perspectives to choose from, which makes it difficult to define what it means to “live” or be “alive” because in perspective something can be alive and in another something may not be considered alive The types of systems and their “predictability” ​ Basic systems - a group of interacting elements that act according to a set of rules to form a unified whole ○​ Bicycle: by looking at some parts of the bicycle, you can tell how the whole system can work. Even if some parts are bent or broken, you can still understand the function of the bicycle. Fewer parts than chaotic systems. ○​ Can predict behavior based on its parts ​ Chaotic systems - dynamic systems that are highly sensitive to initial conditions ○​ Weather: We can predict weather based on initial conditions, however if some things are off slightly, our predictions can be skewed or even wrong. ○​ Technically can predict behavior if you know ALL parts ​ Complex systems - systems with distinct properties that arise from the interactions between parts ○​ Life, Consciousness: To be conscious, neurons interact with each other. However, a single neuron is not consciousness, only a whole system allows for consciousness to occur. To be alive, a whole bunch of systems occur simultaneously between the different parts of your body. But your heart by itself isn’t alive. In order for you to be alive, all systems need to interact. ○​ Cannot predict the behavior based on its parts The rules of complex systems and how you may apply them (to organisms, populations, etc) ​ Rule 1: numbers matter ○​ More numbers allow for more complex features/behaviors ​ Rule 2: interactions are local, not global  ○​ Each component interacts with the components adjacent to it - nothing is in charge ​ Rule 3: the necessity of negative feedback loops ○​ Negative feedback - response reduces initial stimulus (maintains homeostasis) ○​ Positive feedback - response increases initial stimulus ​ Rule 4: the degree of randomness matters ○​ Random agents explore adjacent possibilities ​ ○​ Tradeoff: too much randomness prevents self-organization; not enough prevents flexibility Ask yourself: why is adaptation an emergent feature of populations ​ Adaptation occurs very slowly over years and years. It takes reproduction and small changes along the way for adaptation to take place over the course of generations. ​ An individual's version of adaptation would be responding to stimuli, because we too can respond to our environment, but long term changes will not arise like adaptations. Lecture 3: Heredity and Genetic Exchange What is heredity and the definitions we covered ​ The transmission of DNA from one generation to the next ​ DNA travels vertically from parent to offspring Two types of reproduction (and in which groups they are primarily found) ​ Asexual reproduction: one individual passes entire genome (all genes) to offspring ○​ Typical of prokaryotic ​ Sexual reproduction: two individuals produce offspring by the fusion of gametes with unique combinations of genes ○​ Common across eukaryotes - humans, plants, fungi Familiarize yourself with how to read a sexual life cycle diagram ​ Example (animals): ​ Start with a diploid multicellular organism ​ Goes throgh meiosis which produces gametes ​ Gametes fuse together for fertilization ​ Makes a diploid zygote How variation is produced and why it's important for evolution. All processes that account for variations and for which kinds of organisms. ​ Mutation allows for variation and genetic diversity ​ Important because without mutations, we would go extinct without the ability to change ​ Shuffling also allows for evolution because it creates new combinations of genes or alleles Thought experiment: What are the necessary conditions to observe evolutionary relationships? ​ Presence of heritable traits ​ Genetic variation ​ Phylogeny analysis ​ Shared common ancestor ​ Shared traits or characteristics The logic behind alignments and how they are used to infer evolutionary relationships ​ Alignments give us the ability to quantify changes in DNA sequence/amino acids over time which is used to determine relationships What a phylogeny is, how to read it, and associated vocabulary terms (highlighted terms, “bifurcating branches”, etc) ​ Node: branching point ○​ Represented by a dot ​ Character: trait, phenotype, genotype ○​ Represented by a hatch mark ​ Homology: traits shared due to common ancesty ​ Sister group: share recent common ancestor ○​ Chimps and humans are sister groups ​ Clade: group that contains common ancestors and ALL living descendents ​ Bifurcating branches: each branch splits into two branches at the node What a “highly conserved” gene is ​ Highly conserved gene: the rate at which they change is extremely slow ○​ Change very little over time What a phylogeny is, how we build them, and the assumptions we make to do so ​ Phylogeny: hypothesis of possible evolutionary history which usually depicts the relationships between species ​ Biologists collect data on characteristics of different organisms (DNA sequences) and then analyze similarities and differences to infer evolutionary relationships ​ Assumptions 1.​ Assume common ancestry 2.​ Assume DNA is transferred only by descent 3.​ Assume that once population diverges it no longer exchanges genes (and only diverges into 2) Lecture 4: Life Emerges The event that begins the Earth’s history and why the moon is important for the emergence of complex life ​ Earth’s history begins when Theia smashes into Protoearth and eventually forms the moon ​ The moon stabalizes Earth’s rotation ○​ Before the moon, the Earth wasn’t stable and wobled which caused severe seasonal extremes ○​ Severe seasonal extremes in a very short time (occured quickly) would make it extremely difficult for complex multicellular life to adjust to Define the processes of “accretion” and “planetary differentiation” ​ Accretion: the process of growth that occurs when parts or particles adhere to accumulate on an existing surface/structure ○​ The moon was formed through the process of accretion ​ Planetary differentiation: heavier substances sink; the process by which a planet’s materials separate into distinct layers based on their density and composition Features of Earth that are important to support life ​ Earth’s solid crust is made of heavy metallic elements in order for life to exist ​ All life as we know it is dependent on liquid water ​ Stable climate/regulated temperatures Review: the 6-7 “special” properties of water ​ Cohesion: makes water molecules stick together which causes surface tension ○​ Surface tension allows for some organisms to keep from sinking, such as spiders ​ Adhesion: the attraction of water molecules to other substances ○​ Helps plants transfer water from their roots to their leaves ​ High specific heat: the water resists changes in temperature ○​ Helps to regulate cell temperature ​ Evaporative cooling: reduction in temperature resulting from the evaporation of water from a surface ○​ This is the principle of sweating, or the self-cooling system ​ Lower density as solid: when water becomes ice, it has a lower density ○​ Insulating factor for pond creatures ​ Universal solvent: the substance that is present in the greatest amounts that dissolves numbers of other substances ○​ Allows for vitamins to enter the body for humans through drinking water and most metabolic reactions occur in aqueous solutions Articulate the ways that life is able to increase in complexity over time and how the environment influences this ​ Multicellularity: single-celled organisms began forming colonies which eventually led to multicellular organisms ​ Mutation and genetic variation ​ Cooperation and symbiosis ​ Cumulative evolution ○​ Small incrimental changes over time The three leading hypotheses dissenting why there is H2O on Earth ​ Membranes first ○​ Phospholips spontaneously form structures in polar solvents such as H2O ​ Metabolism first ○​ Life must capture energy to maintain order structures over time ○​ Hydrothermal vents cause chemical reactions consistently and life organized itself around those chemical reactions ​ RNA first ○​ RNA can store genetic information and catalyze reactions What abiogenesis studies and describe (in broad terms) the three “umbrella” hypotheses we discussed ​ Abiogenesis is the study of the emergence of life ○​ Looks at how living entities emerge from non-living entities What is unique about RNA in terms of life’s origins ​ RNA were the first replicators How horizontal gene transfer affects phylogenies and three mechanisms of horizontal gene transfer in bacteria ​ Horizontal gene transfer - DNA may be exchanged between unrelated organisms 1.​ Transduction: transfer by virus through bacterial infection 2.​ Transformation: uptake of foreign DNA form the environment 3.​ Conjugation: when two bacterial cells have cell-cell contact and a plasmid is transferred Review: what an isotope is and why they are useful for dating objects ​ Isotopes: the variant of a chemical element that has the same number of protons ​ You can determine their half life which determines how old/young an object is Ongoing: you should know something (roughly) about the timing of important events, like: Theia impact, liquid water, earliest evidence of life ​ Theia impact, liquid water: ~ 4.5 byo ​ Earliest evidence of life: ~3.8 byo Lecture 5: Single-Celled Life Review the definition of a scientific theory (you can find this on wikipedia) ​ Scientific theory: an explanation of an aspect of the natural world and universe that can be repeatedly tested and corroborated in accordance with the scientific method, using accepted protocols of observation, measurement, and evaluation of results Start thinking about constraints due to common ancestry and how that influences extent organisms (discussed at the beginning of lecture) ​ We use the same 4 base pairs of DNA not because it is the best/most efficient ways, but because of our common ancestry ○​ Once choices are made as organisms evolve, they cannot be unmade and then there are constraints ​ When something evolves in a certain environment, there are constraints ○​ A cactus thrives in dry areas like deserts, but will die in the rainforest In what cases are “highly conserved” genes useful and in what cases are they not ​ Useful: Helps us study fundamental biological processes ○​ 16s rRNA is so highly conserved it led to the discovery of a new domain ​ Not useful: Highly conserved genes evolve slowly, so they are not sensitive enough to detect recent evolutionary changes or differences among closely related species Why “homologies” are necessary for building phylogenies ​ We use homologous DNA sequences to estimate evolutionary relationships ○​ More changes = more distant relationships Continuing: what assumptions do we make when we build phylogenies? (ex. Bifurcating branches, common ancestry, etc.) what happens when these assumptions fail? ​ Assume common ancestry ​ Assume DNA is transferred only by descent ​ Assume that once population diverges it not longer exchanges genes (and only diverges into 2) ​ When these assumptions fail… ○​ Inaccurate trees which may not reflect the true evolutionary history of the organisms ○​ Convergent evolution or reversals may make unrelated organisms appear closely related ○​ Misconstructed phylogenies may fail to predict traits or relationships among organisms accurately The story of 16S rRNA and Woese + Fox – know the three domains, their hypothetical relationships, and how we figured it out ​ Everyone knew there were prokaryotes and eukaryotes ​ Woese & Fox noticed that pretty much everything has ribosomes with the same sequence, the 16s rRNA sequence ○​ Took a bunch of samples from unrelated organisms, sequenced all 16s rRNA sequences, and made an alignment with deep and distant relationships ○​ They found 3 distinct groups ○​ Archea are more closely related to eukarya than bacteria (sister groups, share their most recent common ancestor) ​ Three domains: archaea, bacteria, eukarya Know the starred characteristics on 27.2 – especially in relation to evolutionary relationships Bacteria + Archaea = Prokaryotes Characteristic Bacteria Archaea Eukarya Nuclear envelope Absent Absent Present Membrane enclosed Absent Absent Present organelles Peptidoglycan in cell wall Present Absent Absent RNA polymerase One kind Several kinds Several kinds Introns in genes Very rare Present in some Present in many genes genes Histones associated with Absent Present in some Present DNA species Circular chromosome Present Present Absent Intitiator amino acid for Formylmethionine Methionine Methionine protein synthesis Memory trick for BAE: 1 & 2. NM no p 3. Pep yeah 4, 5, 6. RNA IN HISTOry no 7. CIRCumsized yes 8. A Form of meth What a symbiotic relationship is (and a mutualism) ​ Symbiotic relationship: a close interaction between two different species of organisms where at least one organism benefits from the association, often when both organisms gaining advantages through their interdependence ​ Mutualism: both parties are benefited by their relationships The most important jobs bacteria carry out on Earth ​ Nutrient cycling ​ Decomposition ​ Mutualisms with plants and animals ​ Abundant in oceans providing 20% of oxygen we breathe Why distinguishing bacterial “species” is hard and some methods we use ​ Bacteria can share genes with other bacteria which can make it difficult to differentiate between the different species ○​ Can transfer genetic material NOT by descent which makes things messy ○​ Can’t look at just one gene, you have to look at many genes over time ​ Bacteria reproduce asexually, so it is hard to find characteristics to use in order to distinguish the different species ○​ What is the starting poing of one species becoming 2 distinct species? ○​ Speciation is a continuous process, so at some point you will be able to tell between 2 species, but it is hard to know where to start ​ You can look at their cell structure, cellular metabolism, and differences in cellular components ​ 16s rRNA sequencing can be used to differentiate bacteria at a species level Lecture 6: Cyanobacteria and the Rise of Oxygen How peptidoglycan can be used to distinguish certain bacteria. ​ Peptidoglycan: molecule that is found in the cell walls of bacteria ​ Gram negative: not as much peptidoglycan in the cell walls ​ Gram positive: a lot of peptidoglycan in the cell walls What “oxygenic” photosynthesis is (and how it differs from other kinds). ​ Oxygenic photosynthesis splits water and oxygen becomes our waste product How the O2 in the atmosphere is produced. ​ Great Oxidation Event: cyanobacteria began producing oxygen through oxygenic photosynthesis, releasing it into the atmosphere ​ Oxygen levels gradually increased, leading to the formation of the ozone layer and the eventual support of aerobic life What “nitrogen fixation” is and why it’s important. ​ Nitrogen fixation: converting atmospheric nitrogen to ammonia ​ Organisms that are nitrogen fixers allows us to intake nitrogen in a less complex way (we can’t break down nitrogen in its atmospheric form because it is too difficult to break its triple bond) The importance and consequences of increased O2 availability on living organisms. ​ The increase of O2 in the atmosphere gave rise to larger organisms ○​ Correlation between increase of complex multicellular organisms and increase in O2 ​ Availability of oxygen greatly increased the free energy available to living organisms (glycolysis produces little ATP, O2 has much higher bond energy) ○​ Gave rise to the evolution of the mitochondria (aerobic bacteria) because O2 was able to be used to generate even more ATP than before ○​ Emergence of eukaryotes (complex cell type) ○​ Support of complex multicellular life, which led to a major undocumented extinction of anaerobic organisms Reasons why O2 seems a likely candidate for free energy in organisms that have glucose. ​ Oxygen has a high electronegativity, which allows it to act as the terminal electron acceptor in the electron transport chain ○​ This allows for a significant release of energy as electrons move down their electrochemical gradient ​ Oxygen is highly abundant in the Earth’s atmosphere which makes it a practical choice  ​ Oxygen gives off more energy/produces more ATP than glycolysis Facts that support cyanobacteria were the first organisms to perform oxygenic photosynthesis. ​ The ability to split water (ocygenic photosynthesis) evolved only once in the population of cyanobacteria and every organism came from that Important Concepts Lecture 1 ​ Diffusion ​ Electrochemical gradient ​ Voltage & Membrane potential ​ System I & II ​ Learning & Memory (Short term/long term) Lecture 2 ​ Action potential ​ 7 processes of life ​ Systems ​ Complex system rules Lecture 3 Lecture 4 ​ Features of Earth that are important for life ​ Properties of water ​ How the environment influences the complexity of life Lecture 5 ​ Highly conserved genes ​ Assumptions made about phylogenies ​ 16s rRNA / Woese + Fox findings ​ Important jobs of bacteria Lecture 6 ​ How O2 got in the atmosphere ​ Importance of O2 for life ​ Cyanobacteria being the first to perform oxygenic photosynthesis