Fundamentals of Life Final Study Guide PDF

**Module 1** **1.1 Scientific Method** **Science:** is an approach that helps us be objective with our observations on way of understanding the natural world. **Approaches of science:** - **Discovery science** make verifiable observations and measurements of data. - **Hypothesis driven...

**Module 1** **1.1 Scientific Method** **Science:** is an approach that helps us be objective with our observations on way of understanding the natural world. **Approaches of science:** - **Discovery science** make verifiable observations and measurements of data. - **Hypothesis driven scienc**e everything is put the test through the **scientific method.** **Scientific method**: series of steps that scientists use to find the explanation for phenomena, and prove or deny their initial ***hypothesis***. ***Observation, question, hypothesis, experiment or observations and conclusions.*** **Independent variable: **The one you change during your experiment also known as ***manipulated***. **Dependent variable: **The one you measure during the experiment. This is the variable that responds to the changes in the independent variable also known as ***responding*** variable.  **Controlled variables: **Variables you maintain ***constant*** during the experiment so that they don\'t cause an effect on your dependent variable. **Control group:** *is not exposed* to the independent variable. You\'ll compare your experimental group to this one. **Experimental group:** *is exposed* to the independent variable. **1.2 Characteristics of life** Diversity of organisms in the planet, estimates and calculate there are 8.7 species (or types of living organisms) on Earth. **Life**: is an emergent property that includes the following characteristics: ***metabolism, organization, homeostasis, irritability, growth, reproduction and evolution***. - **Metabolism:** describes all the chemical reactions that a living organism does to obtain energy. **Autotrophic**: organisms that obtain their energy from the sun in a process called photosynthesis like *plants, algae and some bacteria*. ***Are able to elaborate their food***. **Heterotrophs:** are organisms that consume carbohydrates and other molecules for energy. Need to obtain food from other organisms, so ***they need to feed*** on them. **Mixotrophs**: That means they can photosynthesize and consume molecules.  - **Organization**: All living things are made of cells. ***Cell*** is the smallest unit of life, which can survive and reproduce on its own. Existing unicellular and multicellular organisms. - **Homeostasis**: ability of organisms to maintain their internal environment stable. *Keeping your internal conditions within a range in order to survive*. - **Irritability**: organisms' capacity of responding to stimuli. - **Growth**: Every organism grows. - **Reproduction**: Organisms have the capacity of reproduction, or in other words, to make another organism like itself. - **Evolution**: Organisms collectively evolve. This means that over time a population of organism's changes. Some changes become fixed and after many generations the population. **1.3 Levels of Organization** ***Of matter.*** - **Atom**: Smallest unit of an element that retains the properties of the element. - **Molecule**: Combination of atoms ***Biological.*** - **Cell**: Smallest unit of life. - **Tissue**: Group of similar cells that do a specific function together. - **Organ**: A unit of interacting tissues. - **Organ system**: Two or more organs interacting to do a specific function. - **Multicellular organism**: Living organism made up of many cells. ***Ecological.*** - **Individual**: Living organism. - **Population**: Members of the same species that live in the same area. - **Species**: Organisms similar enough to reproduce with each other very similar in shape or genetics. - **Community**: Population of different species that live in the same area. (living things) - **Ecosystem**: Community that interacts with the physical environment. (living and non-living things) - **Biosphere**: Sum of all ecosystems including every region of Earth. **Module 2** **2.1 Ecosystems** **Ecology**: branch of biology that studies the interactions between living beings, and the interactions between living beings and the environment that surrounds them. **Biotic factors **are living beings, such as plants, bacteria, animals and fungi. **Abiotic factors** are inanimate things, such as humidity, temperature, wind, sunlight and soil.  **Trophic levels** represent the feeding levels in a food chain. Is a hierarchy of feeding relationships. **Producers** are in charge of entering energy into the trophic chain, all organisms depend directly or indirectly on them. Autotrophs that obtain energy from a non-living source (usually sunlight) and use it to build organic compounds from inorganic materials. *Plants and phytoplankton are the main producers*. **Consumers**  heterotrophs that obtain energy and carbon by feeding on tissues, wastes and remains of producers, and each other. *Consumers can be described by their diet as herbivores, carnivores, omnivores, detritivores, and decomposers*. **Herbivores:** organisms that only consume plants. **Carnivores:** organisms that only consume other animals. **Omnivores:** organisms that eat both plants and animals. **Detritivores:** organisms that consume detritus or dead organic matter. **Decomposers:** detritivores that break down organic matter into simpler compounds. **Chemosynthesis:** process by which some bacteria use hydrogen sulfide (H~2~S) and other inorganic compounds in thermal vents in the ocean to make their food. **2.2 Interspecific and intraspecific biotic relationships** **Interspecific interactions** **Commensalism**: one species benefit and the other is not affected by the interaction.  **Mutualism**: both species benefit. **Interspecific competition**: interaction in which the two species harm each other and occurs when two organisms fight for the same resources. **Predation**: one species (the predator) captures, kills and eats another (the prey), this type of interaction immediately removes a prey from the population. **Parasitism**: one species (the parasite) benefits by feeding on another (the host) without immediately killing it. *Intraspecific interactions* are those that occur within the same species. Two types of these interactions are known: intraspecific ***competition and cooperation*.** **Intraspecific competition.** Occurs when individuals of the same species fight each other for resources that exist in a limited form. **Intraspecific cooperation.** Occurs when individuals of the same species that form a population, help each other; this type of cooperation can result in relationships such as colony, partnership, gregarious associations, and family associations. **Colony:** organisms have a permanent and so close union that they are physically united. They have a division of labor, so that organisms specialize in certain functions ***like corals***. **Society:** organisms live together, are permanent and are dependent on each other. They have a division of labor and a specialization they have a complex communication system that maintains the social structure ***like ants and bees***. **Gregarious associations:** are occasional or temporary large groups of organisms, with or without kinship ties, that have common activities and join together, either to defend themselves, migrate or forage for food ***like herds of mammals***. **Family associations**: partnerships occur between members of a family, may be temporary or may be linked for several generations. Their purpose is for the offspring to learn and be protected, and sometimes to be able to reproduce. **2.3 Food chains** **Energy flows **in an ecosystem. Energy flow models link trophic levels together, showing energy inputs and losses at each trophic level. There are several models such as **food** **chains, food webs** and **energy pyramids. ** **Food chain:** is a simple model of energy flow that represents a sequence of food relationships, in which energy captured by primary producers is transferred to organisms at higher trophic levels it does not attempt to describe all possible trophic relationships between organisms, but merely follows the relationship between a producer and a single chain of consumers. - Are made up of **two to five organisms.** Since the** producers** do not feed on other organisms, **they are always the first organisms** in the food chain, the **subsequent organisms are the consumers**, starting with the *primary consumers*, who are consumed by the *secondary consumers*, who are consumed by the *tertiary consumers*, who feed the *quaternary consumers* (if any). No organism feeds on the last organism in a food web.The** arrows **in a food chain indicate the** direction in which energy flows.** **Food web:** is a model of energy flow that represents a complex network of food relationships between organisms in an ecosystem. It is more accurate, since in general, an organism that participates in one food chain usually participates in other chains as well. Food chains of an ecosystem are connected to each other as a network. ***This type of model helps ecologists predict how ecosystems will respond to a change*** in one or more of their component species.   **Pyramid models:** represent the distribution of energy and matter in an ecosystem and represent, in a general way, ***the way in which energy flows from producers to consumers in an ecosystem***. They can also represent the mass or number of organisms at each trophic level. At each trophic level, 90% of the energy transferred to the next level is lost, ***only 10% of the energy of that level is transferred to the next level***.  **2.4 Ecological niches** **Ecological niche: **refers to the way an specie fits into its environment and the role it plays in the community. Includes: food, abiotic conditions and behavior. **Habitat:** is a description of a physical place, at a particular scale of space and time, where an organism either actually or potentially lives. Endemic and endangered species **2.5 Endemic and endangered species** **Endemic species: **are any species whose geographic range or distribution is confined to a single given area. ***It is considered endemic if it is not found anywhere else in the world***. **Endangered species:** species particularly vulnerable to extinction. **Threatened species:** \"any species which is likely to become an endangered species within the foreseeable future". **Indicator species: **especially intolerant of physical disturbance to their environment. ***They are the first to decline or disappear when conditions change***, so they can provide an early warning of environmental degradation. **Keystone species:** species that has a disproportionately large effect on a community relative to its abundance exert their effect by physically modifying a habitat, rather than through competition or food web effects, are usually referred to as \"***ecosystem engineers***\".  **Anthropogenic species extinction is caused by: *Overexploitation due to overhunting or overharvesting, habitat loss due to human activity and introduction of invasive or alien species outcompeting native species***. **Module 3** **Topic 3.1 Evolution** **Fixity of species:** Species do not change (they remain fixed). Species were created as they are now. However, this is contradicted by evidence regarding the adaptations and evolutionary versions we find today. *Jean-Baptiste Lamarck* concluded that species change over time and do so in three ways: 1. **The complexifying force:** It is driven by a force that makes it become more complex. For him, humans and other large animals descended from microbes that generated increasingly complex organisms. 2. **Principle of use and disuse:** If an organism used an organ to a greater or lesser extent than its ancestors, then the organ would change over the life of the organism. 3. **Inheritance of acquired characteristics:** The changes that an organism goes through during its life are hereditary. ***Charles Darwin***: [Father of Biology]. He embarked on the *Beagle* taking samples of rocks, animals and plants. His trip lasted 5 years and he traveled along part of the coasts of South America, Australia and Africa. He was impressed by the enormous *diversity* of living beings and that each and every one of them *seemed to be perfectly adapted* to their environment by the process of **natural selection**. He proposed the following postulates of the theory of evolution by natural selection: 1. **Individuals within a species vary.** Members of species are a little different. 2. **Traits are heritable.** Variations must be transmitted from parents to children. 3. **Organisms compete for resources and some organisms fail to survive and reproduce.** No environment has enough resources for all organisms. Resources are limited, and if all organisms survived, they would be depleted. 4. **Survival and reproduction are not usually determined by chance.** Some traits will help organisms survive and reproduce, so they will pass them on to their offspring. 5. **Natural selection modifies populations overtime.** Over time, the population changes to have more favorable traits. An individual cannot evolve, it is the population that evolves over many generations. Traits that are favorable and have become fixed in a population are called **adaptations**. **Sexual Selection**: Similar to natural selection. Except in this case, potential sexual partners choose the individual they want to mate with. ***Alfred Russel Wallace***: explorer who asked the same question and came to the same conclusion as Darwin, contributing greatly to the explanation of the process of natural selection. **Artificial Selection:** Today we continue to obtain new varieties of dogs, cats, fruits and vegetables through *selective crossing*. In rocks we can find *fossils*, which are evidence of past life. They give us an idea of what the ancestor of a species may have been like. **Comparative anatomy:** Evolution leaves traces in the anatomy of living organisms. A structure may look very different at first glance, but once we examine it, it becomes clear that it has the same origin. We have the same bones in our arms as in the wings of a bat. Evolution has only modified the shape of the bones to give them a new function. **Embryology:** Vertebrate embryos have many features in common in their early stages of development, suggesting that they evolved from a common ancestor. **Topic 3.2 Biological Diversity** It is estimated that there are around 8.75 million species, however only 1.2 have been described by scientists. This large number of species forms **biological diversity or biodiversity**. **Taxa (singular taxon)**: name we give to a group of organisms that share a set of traits. The *species* is the smallest taxon we have and the most inclusive *domain.* Scientific name: formed by two Latin words that are *genus and species*, they are unique for each specie and we write them underlined or in *italics.* Major groups of life. **Bacteria**: Single-celled organisms found in all habitats on Earth. **Archaea**: Similar to bacteria but with different metabolism and genetics that can be found in extreme environments. **Protozoa**: Unicellular and microscopic organisms found in humid or aquatic environments and sometimes as parasites, they share the same type of cells as us. **Algae**: They can be unicellular or multicellular, they are found in aquatic environments. **Fungi**: Found in virtually any environment, they are not photosynthetic and obtain food by decomposing dead organisms. **Animals**: They present great diversity in species and in their way of feeding, some are vertebrates and other invertebrates. **Plants**: They are mainly terrestrial and carry out the process of photosynthesis. Some are flowering and others do not, they have seeds and a different method of reproduction. **Taxonomy**: branch of biology that names and classifies species. **Phylogeny**: Try to find the evolutionary history of a species or group of them through genealogy generating diagrams called **cladograms,  phylogenetic tree or tree of life**. **Module 4 What is my body and the bodies of other living beings made of?** **4.1 Carbohydrates** The 4 biomolecules in living organisms are: **[carbohydrates]** , **[lipids]** , **[proteins]** and **[nucleic acids]**. Different versions of biomolecules are assembled from building blocks called **[monomers.]** Their **specific** structure and function arises and depends on the **order,** orientation and **interactions** when they come together in larger molecules they are called **[polymers]**. **4.2 Lipids** They are chains of carbon atoms linked to hydrogen atoms: **[lipids.]** Some lipids have 3 fatty acids attached to glycerol, these lipids are called **[triglycerides]**. A fatty acid is a small organic molecule consisting of a long \"tail\" and a head. The tail is **[hydrophobic]** (greasy), and the carboxylated head is **[hydrophilic]** (acidic). **4.3 Proteins** Proteins constitute a group of biomolecules with a variety of functions, some of which are (write an example next to each function): **[Structural (collagen)]**,**[Hormonal (insulin), Immunity (antibodies), Transport (hemoglobin), Sensations (rhodopsin), Movement (actin) and Enzyme (catalase).]** What are the three structures that are always the same in all amino acids: **[a hydrogen atom, an amino group NH ~2~ and a carbonyl group (COOH).]** Amino acids are joined together through **[peptide bonds.]** This happens between the amino group of an **[amino acid]** and the **[carboxyl group]** of another amino acid, which come together to form chains called **[polypeptides.]** Establish the differences between the different structures of a protein: **Primary**: **[Linear series of amino acids]**. **Secondary**: **[The developing polypeptide twists and turns in three dimensions.]** **Tertiary**: **[When the polypeptide forms folds called domains, converting it into a functional molecule]**. **Quaternary**: **[Two or more polypeptide chains closely associated or linked by bonds to each other.]**  The interactions or bonds that maintain the shape of a protein can be broken by changes in pH or temperature, resulting in: **[denaturation.]** **4.4 Nucleic Acids** Each nucleotide consists of: **[5-carbon sugar]** , **[phosphate groups, nitrogenous base]**. DNA has 4 nitrogenous bases : **[adenine, guanine, cytosine]** and **[thymine,]** which is replaced by **[uracil]** in RNA. Create a table to establish the differences between DNA and RNA DNA RNA ------------------- ---------------------------------------- ------------------------------------------------------------------------------ Sugar Deoxyribose Ribose Nitrogenous bases Adenine, thymine, guanine and cytosine Adenine, uracil, guanine and cytosine (thymine is replaced by ***uracil*** ) Chains Double chain Single chain Complete the table according to the information in readings 4.1-4.4. +-------------+-------------+-------------+-------------+-------------+ | Molecule | Monomer | Polymer | Definition | Types / | | | | | / | Examples | | | | | Characteris | | | | | | tics | | +=============+=============+=============+=============+=============+ | **Carbohydr | Sugar | Carbohydrat | Organic | **Cellulose | | ate** | molecule​ | e | compounds | **: | | | | | consisting | present in | | | | | of carbon, | plant | | | | | hydrogen, | cells, it | | | | | and oxygen, | provides | | | | | used by | plants with | | | | | cells as | rigidity | | | | | **structure | and | | | | | **, | structure. | | | | | **fuel, and | | | | | | energy** | *Most | | | | | storage. | abundant | | | | | | organic | | | | | | compound on | | | | | | Earth*. | | | | | | | | | | | | **Sucrose** | | | | | | : | | | | | | \"table | | | | | | sugar.\" | | | | | | Found | | | | | | naturally | | | | | | in many | | | | | | plants. | | | | | | | | | | | | It is | | | | | | extracted | | | | | | mainly from | | | | | | sugarcane. | | | | | | | | | | | | **Starch**: | | | | | | main energy | | | | | | reserve in | | | | | | plants, | | | | | | provides | | | | | | energy. | | | | | | Abundant in | | | | | | corn, rice, | | | | | | wheat, | | | | | | potatoes | | | | | | and tubers. | | | | | | | | | | | | Numerous | | | | | | industrial | | | | | | uses. | | | | | | | | | | | | **Monosacch | | | | | | arides**: | | | | | | simple | | | | | | sugars, | | | | | | they are | | | | | | sweet. | | | | | | Examples: | | | | | | **glucose** | | | | | | , | | | | | | the main | | | | | | source of | | | | | | energy for | | | | | | cells, | | | | | | **ribose** | | | | | | and | | | | | | **deoxyribo | | | | | | se,** | | | | | | components | | | | | | of the | | | | | | nucleotide | | | | | | monomers of | | | | | | RNA and | | | | | | DNA. | | | | | | **Fructose* | | | | | | * | | | | | | and | | | | | | **galactose | | | | | | **. | | | | | | | | | | | | **Disacchar | | | | | | ides**: | | | | | | They are | | | | | | formed by | | | | | | two sugar | | | | | | monomers | | | | | | such as | | | | | | **lactose** | | | | | | (glucose + | | | | | | galactose) | | | | | | and | | | | | | **sucrose** | | | | | | (glucose + | | | | | | fructose). | | | | | | | | | | | | **Oligosacc | | | | | | harides**: | | | | | | are linked | | | | | | to lipids | | | | | | (glycolipid | | | | | | s) | | | | | | or proteins | | | | | | (glycoprote | | | | | | ins) | | | | | | important | | | | | | functions | | | | | | in the | | | | | | immune | | | | | | system. | | | | | | | | | | | | **Polysacch | | | | | | arides**: | | | | | | chains of | | | | | | hundreds or | | | | | | thousands | | | | | | of | | | | | | monosacchar | | | | | | ide | | | | | | monomers. | | | | | | | | | | | | **Cellulose | | | | | | **: | | | | | | The most | | | | | | abundant | | | | | | biological | | | | | | molecule on | | | | | | Earth. | | | | | | Humans and | | | | | | other | | | | | | mammals do | | | | | | not produce | | | | | | the enzymes | | | | | | needed to | | | | | | break down | | | | | | cellulose | | | | | | to create | | | | | | *fiber* in | | | | | | our food. | | | | | | | | | | | | **Starch:** | | | | | | stores | | | | | | sugars | | | | | | inside | | | | | | plant cells | | | | | | | | | | | | **Glycogen: | | | | | | ** | | | | | | is a sugar | | | | | | storage | | | | | | facility in | | | | | | animals in | | | | | | *the liver* | | | | | | and | | | | | | *muscle.* | +-------------+-------------+-------------+-------------+-------------+ | **Lipid** | *Fatty | Lipids and | Greasy, | Saturated: | | | acids*: | fats | oily or | they only | | | chains of | | waxy | have single | | | carbon | | organic | bonds, | | | atoms | | compounds. | completely | | | linked with | | They vary | saturated | | | hydrogen | | in | with | | | atoms | | structure, | hydrogen | | | | | but all are | atoms, | | | | | **hydrophob | flexible | | | | | ic**, | and move | | | | | meaning | freely, | | | | | they repel | ***liquid | | | | | water | at body | | | | | (*insoluble | temperature | | | | | in water*). | but solid | | | | | | at room | | | | | *They make | temperature | | | | | up the | ***. | | | | | structure | | | | | | of cell | They are | | | | | membranes*, | found | | | | | they are | naturally | | | | | *energy | in many | | | | | reserves* | foods, most | | | | | and compose | of them of | | | | | *signaling | animal | | | | | molecules*. | origin, | | | | | | including | | | | | **Animal | meat and | | | | | fats** are | dairy | | | | | found in | products. | | | | | foods such | These types | | | | | as meat and | of fats are | | | | | butter, | generally | | | | | while most | ***consider | | | | | **vegetable | ed | | | | | fats** are | unhealthy** | | | | | oils, such | *. | | | | | as olive | | | | | | oil and | Unsaturated | | | | | peanut oil. | : | | | | | | there are | | | | | | one or more | | | | | | double | | | | | | bonds | | | | | | between the | | | | | | carbons, | | | | | | which | | | | | | limits | | | | | | their | | | | | | flexibility | | | | | |. | | | | | | | | | | | | Cis fats: | | | | | | **These | | | | | | types of | | | | | | fats are | | | | | | considered | | | | | | healthy**, | | | | | | such as | | | | | | *omega-3* | | | | | | and | | | | | | *omega-6*, | | | | | | and are | | | | | | found in | | | | | | fish and | | | | | | vegetable | | | | | | oils. | | | | | | | | | | | | Trans fats: | | | | | | do not | | | | | | exist | | | | | | naturally, | | | | | | they are | | | | | | formed by | | | | | | the | | | | | | hydrogenati | | | | | | on | | | | | | of | | | | | | vegetable | | | | | | oils, for | | | | | | example | | | | | | *margarine* | | | | | | , | | | | | | ***they | | | | | | increase | | | | | | the risk of | | | | | | cardiovascu | | | | | | lar | | | | | | diseases by | | | | | | negatively | | | | | | affecting | | | | | | cholesterol | | | | | | levels in | | | | | | the blood | | | | | | and the | | | | | | function of | | | | | | arteries | | | | | | and | | | | | | veins.*** | +-------------+-------------+-------------+-------------+-------------+ | **Protein** | Amino acids | Polypeptide | Biomolecule | Structural | | | | (protein) | s | (collagen): | | | | | that | fibrous | | | | | participate | protein | | | | | in all | found in | | | | | processes | cartilage, | | | | | that | tendons, | | | | | sustain | skin and | | | | | life. They | other | | | | | are formed | tissues. | | | | | by carbon | Most | | | | | (C), | abundant | | | | | hydrogen | protein in | | | | | (H), oxygen | the human | | | | | (O), | body. | | | | | nitrogen | | | | | | (N), | Hormonal | | | | | phosphorus | (insulin): | | | | | (P), sulfur | produced by | | | | | (S) and | the | | | | | commonly | pancreas, | | | | | contain | controls | | | | | iron (Fe), | the amount | | | | | magnesium | of sugar in | | | | | (Mg). | blood. | | | | | | | | | | | | Immunity | | | | | | (Antibodies | | | | | | ) | | | | | | produced by | | | | | | the immune | | | | | | system to | | | | | | fight | | | | | | foreign | | | | | | substances. | | | | | | | | | | | | Transport | | | | | | (Hemoglobin | | | | | | ): | | | | | | present in | | | | | | red blood | | | | | | cells | | | | | | transportin | | | | | | g | | | | | | oxygen from | | | | | | the lungs | | | | | | to the | | | | | | tissues and | | | | | | organs of | | | | | | the body; | | | | | | it also | | | | | | transports | | | | | | carbon | | | | | | dioxide | | | | | | back to the | | | | | | lungs | | | | | | | | | | | | Sensations | | | | | | (rhodopsin) | | | | | | : | | | | | | photorecept | | | | | | or | | | | | | that | | | | | | absorbs | | | | | | light in | | | | | | the retina. | | | | | | | | | | | | Movement | | | | | | (actin): | | | | | | gives shape | | | | | | to the | | | | | | cell, | | | | | | participate | | | | | | s | | | | | | in cellular | | | | | | movements | | | | | | and muscle | | | | | | contraction | | | | | |. | | | | | | | | | | | | Enzyme | | | | | | (catalase): | | | | | | involved in | | | | | | the | | | | | | destruction | | | | | | of hydrogen | | | | | | peroxide | | | | | | generated | | | | | | during | | | | | | metabolism. | +-------------+-------------+-------------+-------------+-------------+ | **Nucleic | Nucleotides | Nucleic | Energy | DNA: | | Acid** | | Acid | carriers, | ***Deoxyrib | | | | | enzyme | onucleic | | | | | auxiliaries | acid***. It | | | | | , | is | | | | | chemical | distributed | | | | | messengers | in the | | | | | and | chromosomes | | | | | subunits of | of species. | | | | | DNA and | Genes are | | | | | RNA. | segments of | | | | | | DNA that | | | | | | contain the | | | | | | information | | | | | | necessary | | | | | | to produce | | | | | | a protein. | | | | | | | | | | | | Their | | | | | | chains are | | | | | | joined by | | | | | | hydrogen | | | | | | bonds. | | | | | | | | | | | | RNA: | | | | | | ***Ribonucl | | | | | | eic | | | | | | acid***. | | | | | | Different | | | | | | types of | | | | | | RNA | | | | | | interact | | | | | | with DNA | | | | | | during | | | | | | protein | | | | | | synthesis. | +-------------+-------------+-------------+-------------+-------------+  **Module 5 How did life originate on Earth?** 5.1 Early ideas and theories of the origin of life Theories on the origin of life +-----------------------+-----------------------+-----------------------+ | **Theory** | **Author** | **Characteristics** | +=======================+=======================+=======================+ | **Creationism** | Philosophers | The origin of life | | | | thanks to a divine | | | | creation/intervention | | | | , | | | | life began thanks to | | | | a god or gods | | | | creating life. | +-----------------------+-----------------------+-----------------------+ | **Spontaneous | Johan B. van Helmont | Life can arise from | | generation** | | inanimate matter and | | | | seemingly emerge from | | | | nothing. | +-----------------------+-----------------------+-----------------------+ | **Rejection of | Francesco Redi and | **Redi**: This | | spontaneous | Louis Pasteur | experiment proves | | generation** | | that maggots come | | | | from flies and do not | | | | appear spontaneously | | | | from rotting meat. | | | | | | | | **Pasteur**: He | | | | designed a swan-neck | | | | flask in which he | | | | placed a solution | | | | with nutrients to | | | | determine the causes | | | | of bacterial growth. | +-----------------------+-----------------------+-----------------------+ | **Panspermia** | Augustus Arrhenius | Life appeared on | | | | Earth thanks to a | | | | bacteria or spore | | | | that came from outer | | | | space with life and | | | | arrived on Earth in a | | | | meteorite. | +-----------------------+-----------------------+-----------------------+ | **Primitive Earth** | Oparin and Haldane | On the primitive | | | | Earth, the | | | | biomolecules of life | | | | could have been | | | | formed. | +-----------------------+-----------------------+-----------------------+ | **Simulation of the | Miller-Urey | It was intended to | | early Earth** | | simulate the | | | | conditions of the | | | | early Earth that | | | | Oparin-Haldane | | | | proposed in their | | | | hypothesis. | +-----------------------+-----------------------+-----------------------+ 5\. 2 Abiogenesis and chemical evolution The atmosphere was rich in gases such as ***methane, ammonia, water vapor, and carbon dioxide, but lacked free oxygen***. These gases, together with the energy provided by ultraviolet radiation and cosmic rays, would have favored the formation of complex biomolecules from simpler molecules. **Miller-Urey** experimentally demonstrated that organic molecules, crucial for life, could arise from simple inorganic precursors under conditions similar to those proposed by the **Oparin-Haldane** hypothesis, since in just 1 week of their experiment *they managed to find the production of various organic compounds, including amino acids, which are the basic components of proteins, lipids and other organic molecules such as urea, cytosine and uracil*. **Antonio Lazcano Araujo**, a prominent Mexican biologist and leading researcher in the field of abiogenesis, proposes that the origin of life involves the following events: 1. **Chemical evolution**: Gradual process of inorganic elements leading to the formation of organic compounds. 2. **RNA world hypothesis:** RNA is made from DNA. And RNA acts as a template to make proteins. According to this hypothesis, it could have arisen in reverse, with DNA appearing again as a more stable molecule. 3. **Primitive metabolism:** simple organic molecules could have undergone reactions that produced the energy and essential biomolecules necessary for the emergence of life. 4. **The first membranes:** Lipids are arranged in a bubble-like shape (protocell). These steps are vital for life to begin. Providing the reactions primitive metabolic and genetic information a place to develop without intervention from the outside environment.** ** **Module 6. How are living beings structured at the most fundamental level?** 6.1 Cell theory **Robert Hooke** First person to observe (dead) cells, analyzing cork under a microscope and discovering that it consisted of many \"cells\" that were compartments which he called cells (as a biological term). ---------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- **Antoni van Leeuwenhoek** The first person to observe living cells, he revealed the existence of tiny organisms in rainwater, insects, cloth, sperm, feces and others which he called \"animalcula.\" **Matthias Scheliden** He showed that plant tissues are composed of cells and their products. **Theodor Schwann** He showed that animal tissues are composed of cells and their products. **Postulates of cell theory:** 1. Every living organism consists of one or more cells. 2. The cell is the basic unit of life. Cells are alive individually, even though they are part of a multicellular organism. 3. All living cells arise by division of pre-existing cells. 4. Cells contain hereditary material (DNA), which they transmit to their descendants during the process of reproduction. 6.2 Prokaryotic and eukaryotic cell. Organisms are made up of two types of cells **Prokaryotes**: They lack a nucleus. **Eukaryotes**: They have a nucleus inside them. Main differences between prokaryotic and eukaryotic cells **Prokaryote** **Eukaryote** ---------------------- ------------------------------------------------ -------------------------------------------------- Size They are smaller and morphologically simpler They are larger and morphologically more complex Representatives Bacteria and archaea Protists, fungi, plants and animals Number of cells Unicellular Multicellular Organelles Without nucleus or other membranous organelles With nucleus and other membranous organelles Metabolic site Cytoplasm Cytoplasm and organelles Compartmentalization Without compartments With compartments 6.3 Endosymbiosis. **Lynn Margulis**: proposed that the symbiotic association of free-living prokaryotes gave rise to the mitochondrion and chloroplast. **Symbiosis**: relationship in which one organism lives inside another and both benefit. It suggests that the first mitochondria and chloroplasts were prokaryotic cells engulfed by larger prokaryotes. If the larger cell incorporated a prokaryote (aerobic bacteria) that acted as a mitochondrion, it could obtain energy in the form of ATP. If it incorporated a prokaryote (cyanobacteria) that acted as a chloroplast, it could carry out photosynthesis to produce sugars. In return, they obtained a stable environment and nutrients. ***Evidence of endosymbiosis*** - Both the chloroplast and the mitochondrion have a double membrane. - They have their own DNA. - The DNA of mitochondria and chloroplasts is circular, like that of current prokaryotes. - They have their own protein synthesis machinery. - They can multiply by binary fission, just as current prokaryotes do. 6.4 Difference between bacteria, plant and animal cells Presence of cellular structures in different cell types 6.5 Structure and function of cell organelles **Organelle** **Function** --------------------------------------------- ------------------------------ --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Shared by all cells Plasma membrane It surrounds the cell, separates it from the external environment, and controls the movement of substances in and out. Cytoplasm Gelatinous mixture of water and solutes inside a cell, where the greatest number of metabolic reactions occur. Ribosomes Protein synthesis. DNA Genetic material of the cell. Shared between animal and plant cells Nucleus Controls all cellular activities; organelle with a double membrane (nuclear envelope) and with thousands of nuclear pores, keeps the cell\'s DNA safe and controls the passage of certain molecules. They may have one or more **nucleoli**, which are dense regions with proteins and nucleic acids, where the subunits of the ribosomes are produced. Vesicles Membranous sacs that transport substances within the cell. Vacuoles Larger vesicles, storage sites for waste, liquids, remains, toxins or food. Smooth endoplasmic reticulum Membranous sacs and tubes that continue from the nuclear envelope. Produces and stores lipids and can detoxify the cell. Rough endoplasmic reticulum It has ribosomes on its surface, which produce proteins. Golgi apparatus Membrane system that puts the finishing touches on proteins and lipids released from the endoplasmic reticulum. It sorts and packages them into vesicles. Mitochondria Organelle that produces ATP through aerobic respiration. Cytoskeleton Interconnected protein filaments reinforce, organize and give mobility to cellular structures. Exclusive to plant cells Chloroplast They carry out photosynthesis in plants and photosynthetic protists. Central vacuole Filled with liquids, it occupies most of the volume and maintains the cell\'s water balance. Exclusive to animal cell Lysosomes Type of vesicle in animal cells that contain enzymes that break down waste, cellular debris, or microbes, so they can be considered the cell\'s garbage cans. Centrioles Component of the cytoskeleton, in the shape of a cylinder, involved in cell division. Shared between plant and prokaryote cells Cell wall It encloses the cell, protects it and helps it maintain its structure. Some bacteria have peptidoglycans (proteins plus sugars), while archaea have a wall formed by proteins or glycoproteins. The walls of plant cells, on the other hand, have cellulose. Shared between animal and prokaryotic cells Flagella Long, thin cellular structures used for movement. Found in many prokaryotes and in some animal eukaryotic cells, such as sperm.  Differences Between Plant and Animal Cells 6.6 Virus Noncellular infectious particle that can replicate only within a living cell. ***It is an obligate intracellular parasite***. It has no ribosomes or other metabolic machinery and is not capable of producing ATP. To replicate, the virus must insert its genetic material into a cell of a specific host organism. They are the most abundant infectious agents on the planet, examples: influenza AH1N1 and the SARS-CoV2 coronavirus. It is important to study them to obtain information on how to *control diseases*, because they can give us clues to *evolutionary mechanisms* and for their use in *medical applications* since they have the potential to be used as tools to treat diseases, to be used in gene therapy, in cancer treatments and to develop new vaccines. **Characteristics**: **Small size.** They are not visible with light microscopes, although they are visible with electron microscopes. **Components.** All viruses contain **genetic material**, either DNA or RNA, have a protein-based **capsid**, and have few or no enzymes. They do not contain cytoplasm or a plasma membrane. Some have an additional layer of covering around the capsid. **Structural diversity.** They are very diverse in shape and structure: some capsules are simple and spherical and others are more complex. **Genomic diversity.** Some have only four genes, while others have 2,500 genes. In comparison, the human genome contains about 20,500 genes.   **Mechanism of infection** They enter our body through mucous membranes (eyes, nose, mouth, penis, vagina or anus). Some enter through mosquito or tick bites. Steps of infection: 1. **Binding.** Proteins on viral particles chemically recognize and attach to specific receptors on the surface of the host cell. 2. **Entry.** The viral particle or its genetic material crosses the plasma membrane of a host cell and enters the cytoplasm. 3. **Replication and synthesis.** Viral DNA or RNA directs the host to produce viral nucleic acids and viral proteins. 4. **Assembly.** Viral components self-assemble into new viral particles. 5. **Release.** New viral particles are released from the cell.   **Common viral diseases:** Most cause mild symptoms, like adenoviruses that infect the upper respiratory system and cause the common cold. Sometimes they can be more persistent, such as some herpes viruses that cause cold sores, genital herpes, mononucleosis, or chickenpox. Typically, the infection causes symptoms that disappear quickly, but the virus remains dormant in the body and can flare up again later. Measles, mumps, rubella and chickenpox are childhood viral diseases that until recently were common throughout the world. Today, most children living in developed countries have been vaccinated against these diseases. Vaccination prepares the body to fight a specific pathogen. **Module 7** **7.1 Cell Cycle** **Interphase** (cell is not under division): Is the series of events that occur as a cell grows, replicates its DNA, and divides into two daughter cells.  Three main phases: 1. **G1**: Phase, of major growth, the cell doubles its organelles and accumulates materials needed for DNA synthesis. 2. **S (Synthesis)**: DNA replication occurs in this phase to duplicate its genetic material. 3. **G2** (**maturation)**: The cell continues to grow, synthesizes more proteins, and prepares for division. **Phase M**: the cell go through reproduction, which is **mitosis or meiosis**. They include the following stages: - *Prophase, Metaphase, Anaphase, Telophase* (for nuclear division) and *cytokinesis* (to divide the cytoplasm). Sometimes, the cell dies. And it gets darker than this: sometimes the body programes a specific cell to die in a proccess known as **apoptosis**. Apoptosis is like the cell's graceful exit strategy. Its importance are the following points: - **Development**: During the development of embryos, apoptosis shapes tissues by removing excess cells. For example removes extra tissue. - **Homeostasis**: apoptosis balances cell production and loss. - **Defense**: Apoptosis eliminates cells with irreparable DNA damage or infected. - **Preventing Cancer**: Faulty apoptosis can lead to uncontrolled cell growth (cancer). Proper apoptosis helps prevent this . **7.2 DNA Replication** Is an important process that happens during the S phase. It ensures that every cell gets the same instructions for building proteins and carrying out essential functions.   DNA replication follows 3 steps driven by three different enzymes (biological catalyzers that promote chemical reactions): 1. **DNA Helicase**: Unwind "open" the Double by breaking the hydrogen bonds between the base pairs (A-T and C-G). 2. **DNA Polymerase**: Copy the strands adding the complementary base to each base it finds building two identical daughter strands. 3. **DNA Ligase**: One strand is copied continuously (***Leading***). The other strand is copied in sections called Okazaki fragments and form the ***lagging*** strand. The enzyme "ligate" the fragments with primers and seals the double helixes.   Sometimes, DNA polymerase makes a mistake: it doesn\'t add the correct complementary base. This is a mistake that can lead to ***mutations***.   DNA replication is a fundamental process in live. Its importance is declared in the following arguments: - **Genetic Continuity**: DNA replication ensures that genetic information is faithfully passed from one generation of cells to the next. - **Evolution and Adaptation**: Some mutations are harmful, but others drive evolution. - **Cancer and Replication Errors**: Some mutations contribute to cancer development. Understanding DNA replication helps researchers study cancer and develop targeted therapies **7.3 Mitosis** **Chromatin: *Disperse form of DNA*** when the cell is not under division. **Chromosome:** ***Condense form of DNA*** during cellular division. - **Chromatid:** It\'s one of the two identical copies of a condensed DNA strand.  - **Centromere**: Specialized region of the chromosome that holds the sister chromatids together during cell division. - **Telomeres:** Regions of repetitive nucleotide sequences located at the ends of chromosomes. They protect the ends of the chromosomes from deterioration and fusion with neighboring chromosomes. - The division stage is known as **mitosis**. 1. **Prophase**: - Breakdown of the cell membrane. - Chromatin condense into chromosomes. - Centrioles migrate into the poles of the cell. - Mitotic spindle is formed. 2. **Metaphase**: - Chromosomes get aligned by the equator of the cell. - Microtubules of the mitotic spindle get anchored by the centromere of each chromosome. 3. **Anaphase**: - Microtubules of the mitotic spindle break the chromosomes and pull them into the poles of the cell. - Early citokinesis begins. 4. **Telophase**: (Opposite to prophase) - Nuclear membrane regenerates. - Chromosomes decondense forming chromatin again. - Centrioles lose their function and disappear. - Mitotic spindle disappear. - Cytokinesis continues. 5. **Cytokinesis**: - Complete division of the cytoplasm leaving two new and independent cells that enter into interphase. **7.4 Meiosis** **Sexual reproduction** requires a different mechanism for nuclear division, **meiosis**, reduce the number of chromosomes at the half. When a **diploid** cell undergoes meiosis, it produces **haploid** cells. **Ploidy**: refers to the number of sets of chromosomes present in the nucleus of a cell.  **Haploid (n)**: Haploid cells contain one complete set of chromosomes. **Diploid (2n)**: Diploid cells contain two complete sets of chromosomes. **Polyploid (\>2n)**: Polyploid cells contain more than two sets of chromosomes. The phases of meiosis occur in the same way as in mitosis with the only difference that **in prophase I** of **meiosis I** the overlap of chromosomes and the crossing over of alleles occurs.  **Mitosis** **Meiosis** ----------------------------------------- --------------------------------------------------------------------------------- 1 stage 2 stages (Meiosis I and Meiosis II) Produce 2 cells Produce 4 cells Cells produced are genetically the same Cells produced are genetically different (because the crossing over of alleles) Produce diploid cells Produce haploid cells Used for growth, repair and replace Used to make gametes (sexual cells) **Module 9 Genetics** **9.1 Mendel\'s Laws** **Gregor Mendel** was an Austrian monk. He was very interested in science and in particular he was curious about how traits (characteristics) are transferred from one generation to the next. To study this he started an experiment with peas plants. Mendel performed what we now call ***monohybrid crosses*** studying the inheritance of a single trait. ***Chromosomes*** are condensed structures formed by DNA molecules. In chromosomes we find ***genes***.  **Genes** contain sequences of DNA that encode specific proteins or traits. These proteins influence our immune system, hormone production, and physical features like hair color, height, blood group, and eye color. In other words, our genes are what make us us.   **Allele** is a different version of the same gene.  We inherit one set of chromosomes from our mother and another set from our father. This means we can have two different alleles for the same gene.  **Genotype**: The genetic information of an organism, the combination of alleles it has. **Phenotype**: Observable characteristics of an organism. **Homozygous**: Organism that has the same allele on each chromosome. Example BB or bb. **Heterozygous**: Organism that has different pairs of alleles. Example Bb **Dominant**: A dominant allele hides the expression of a recessive allele. This means that if a person has the genotype BB or Bb (for brown eyes), that person will have brown eyes, even in the genotype where they have the allele for blue eyes. **Recessive**: It is not observable in heterozygous organisms. These are alleles that are only observable in organisms with homozygous genotype such as bb. **Codominance**: happens when both alleles are expressed in the heterozygote. **Incomplete dominance**: happens when the heterozygote is intermediate between the two homozygotes. **Mendel\'s Laws** 1. **Law of Segregation:** each individual organism carries two alleles for each trait (one from each parent). During **meiosis**, these alleles segregate, ensuring that each gamete (sperm or egg) contains only one allele. This separation of alleles during gamete formation leads to the inheritance of specific traits. 2. **Independent Assortment**: different traits are inherited independently of each other. 3. **Law of Dominance**: some alleles are **dominant**, while others are **recessive**. Beyond natural selection, the Modern Synthesis recognized three additional evolutionary forces: - **Mutation**: Central to natural selection, mutation makes genetic variation. - **Gene Flow**: Movement of genetic information between populations. - **Genetic Drift**: Random changes in allele frequencies due to small population sizes. **9.2 Monohybrid crosses** To make predictions of Monohybrid Crosses we use **Punnett squares**, devised by the British geneticist **Reginald Punnett**. **Autosomal disorders** are a group of genetic conditions or diseases that result from mutations or abnormalities in genes located on the autosomes (non-sex chromosomes). A single copy of the mutated gene (from one parent) is sufficient to cause the condition. **Autosomal Recessive Disorder**s both copies of the gene must be mutated for the condition to manifest. **9.3 Sex-linked hereditary traits** There are two main biological sexes: - ***XX*** chromosomes with female genitals - ***XY* **chromosomes with male genitals  **Red-Green Color Blindness.** Males are affected more often than females because they have only one *X* chromosome. Females can be carriers (heterozygous) and pass the gene to their offspring. For females to present red-green color blindness they would have to have both *X *chromosomes caring the gene. **Hemophilia A** is a disorder that interferes with the blood clotting. The gene responsible for hemophilia A is also located on the *X* chromosome. This disorder also affects biological males more than females. **Module 10 energy** **10.1 Photosynthesis** **Metabolism** **Catabolism:** Catabolic reactions are those used by an organism to destroy large molecules, obtaining small molecules to reuse. Digestion, for example, is a catabolic biochemical process that the human body uses to obtain monomers of different biomolecules. **Anabolism:** Anabolic reactions are those used by an organism to assemble new biomolecules from monomers in reserve. The creation of new muscle mass and DNA replication are examples of anabolic reactions. **Photosynthesis:** The energy of our ecosystems reaches the earth in the form of sunlight and is captured in chemical compounds by plants through photosynthesis. This reaction occurs in the leaves of plants, in cellular organelles known as chloroplasts. During photosynthesis, carbon (CO~2~) moves from the environment to organisms that incorporate it into sugars.  **Photosynthesis** is a metabolic pathway that uses light to drive the assembly of carbohydrates---sugars---from carbon dioxide and water. The sugars can be stored as starches for later use, remodeled into other compounds, or broken down to release energy held in their bonds. **General Equation**: 6H~2~O+ 6CO~2~ \-\-\-\-\-\--C~6~H~12~O~6~ + 6O~2~ **Stages**: **Light dependent reactions** To convert carbon dioxide (CO~2~) into glucose (C~6~H~12~O~6~), a source of hydrogen is needed. Water (H~2~O) is one of the most accessible sources of hydrogen on Earth To access the hydrogen, it first needs to be removed from the water. **Photolysis** is the stage of photosynthesis in which water is split by light. The energy in photons is used to split water molecules, generating hydrogen ions, electrons, and oxygen. This occurs in the thylakoids of chloroplasts. The oxygen is released as a waste product. **Light-Independent Reactions (Calvin Cycle)** The ATP is then used, along with the hydrogen and electrons removed from the water, in the light-independent reactions, during which carbon fixation occurs. Carbon fixation is the conversion of inorganic carbon to organic carbon. In other words, the carbon dioxide from the air is combined with hydrogen using the energy from ATP to form glucose and other carbon compounds. These reactions do not require light and take place in the stroma of chloroplast.  **Oxygen levels in atmosphere** Photosynthesis is one of the most important biological processes on Earth. When cyanobacteria evolved the ability to use the energy from the sun to convert carbon dioxide to glucose and other carbon compounds, life on Earth was forever changed. **10.2 Cell Respiration**  **Autotrophs:** harvest energy directly from the environment and store it in the form of sugars and other carbohydrates. They use energy stored in sugars to power reactions that sustain life. **Heterotrophs**: In order to use the energy stored in sugars, cells must first transfer it to molecules ---especially ATP---that can participate directly in these reactions. This is where respiration takes place.  *Oxygen-requiring cellular respiration* is called **aerobic respiration** that means "breathing air,". **Cellular respiration:** is a metabolic pathway that takes place in the cytoplasm (anaerobic or fermentation) or in the cytoplasm and mitochondria (aerobic) using carbohydrates (sugars) to produce energy in the form of ATP. **General Equation**: C~6~H~12~O~6~ + 6O~2~\-\-\-\-\-\-- 6H~2~O+ 6CO~2~ + ATP These equations mean that glucose and oxygen are converted to carbon dioxide and water, for a yield of ATP. Is a complex series of metabolic pathways and cycles that break down these carbon compounds, releasing energy which is then used to produce the ATP molecules that power all other processes in the cell. It consists of many reactions that occur in four stages: *glycolysis, acetyl--CoA formation (preparatory phase), the citric acid cycle (Krebs cycle), and electron transfer phosphorylation (oxidative phosphorylation)*. Animals use **aerobic respiration** (it needs oxygen) to break down sugars and release **ATP** and heat. Sugar comes from the plants and animals we eat. We can store this energy as **glycogen or lipids**. Bacteria and yeast use **anaerobic respiration** (without oxygen) to break down sugars for energy, releasing CO2 and alcohol in the process. Features widely used in cooking and beer production. **Glycolysis**: takes place in the cytoplasm of cells. A molecule of glucose is broken down into smaller molecules. This process releases a small amount of energy and forms two molecules called ***pyruvate***.  **Preparatory phase**: pyruvate is further broken down into a molecule called ***acetyl-CoA***. This step is crucial because it prepares the molecules for the next stages of aerobic respiration. **Krebs Cycle**: happens in the mitochondria and involves a series of chemical reactions that fully break down the acetyl-CoA molecules. As a result, more energy is released in the form of electrons, and small energy-carrying molecules like NADH and FADH~2~ are produced. **Oxidative Phosphorylation**: takes place in the mitochondria and is like the grand finale of the energy production process. The electrons carried by NADH and FADH~2~ from the previous stages are shuttled along a chain of proteins embedded in the inner mitochondrial membrane. As the electrons move, they release energy, which is used to pump protons across the membrane, creating a proton gradient. This gradient drives the production of ATP. **Anaerobic respiration** **or lactic fermentation** in humans. *Occurs in the absence of oxygen in the cytoplasm of the cell*. Only glucose and other carbohydrates can be used as respiratory substrates and a relatively small amount of ATP is the yield with only a net (overall) gain of two molecules. The waste product of anaerobic respiration in humans is **lactate**. Most organisms, including humans, carry out fermentation with chemical reactions that convert pyruvic acid to **lactic acid**. Provides quick use power (90sec). **Alcoholic fermentation**: yeasts and some other organisms use it to produce ethanol and CO2 (Preparation of alcoholic beverages, bread dough).