Bio notes.pdf

Lecture 1 - 1.1 71,2 - Properties of Life 1. Metabolism ○ The transformations of matter and energy take place inside organisms. ○ Ex: food into energy ○ These transformations can be understood using the principles of chemistry and physics that we observe i...

Lecture 1 - 1.1 71,2 - Properties of Life 1. Metabolism ○ The transformations of matter and energy take place inside organisms. ○ Ex: food into energy ○ These transformations can be understood using the principles of chemistry and physics that we observe in non-living systems. + What is considered life? Was thought to be some sort of force/energy! We now believe, for the purposes of biology, that the properties of life emerge from complicated relationships among non-living parts; a relational concept. Energy transformations in a living cell are fundamentally the same as those that occur outside living organisms; both can be understood by the same types of processes: the laws of thermodynamics. Isolated properties of a cell may be functional on their own, but they are not living. Ex: mitochondria in a test tube - non-living - vs. in a cell - living -. The interaction of non-living things - such as parts of a cell - defines life. 1.5. Self movement/growth Living things are usually capable of self movement - throwing a ball - or sometimes as well/instead of growth - plant -. 2. Selective barriers ○ They let some things across, not others. ○ Ex: exterior of a cell; very selectively allows some things in and doesn't allow other things through; inside differs from outside. 2. Selective barriers Lets some things across, not others Ex: exterior of a cell; very selectively allows some things in and doesn't allow other things through; inside differs from outside Homeostasis: An organism's ability to maintain a different internal environment compared to an external environment. There will be less variation in internal conditions than external conditions. Ex: Your body temperature tends to stay about the same, despite the external temperature. One definition of life: Life is metabolism inside a selective barrier. 3. Responsiveness to stimuli Living things are responsive to stimuli. ○ Ex: A plant/seed is responsive to water, to gravity - grows roots down and leaves up - , and sunlight. 4. Reproduction Living things reproduce. The offspring will resemble the parent - 3 - but will not necessarily be identical. Asexual vs sexual reproduction. Genetic transmission of traits is due to DNA sequences being transmitted. DNA is packed into chromosomes. Genetic tree - Phylogenetic tree - Shows the relationship between species. How far away 2 species/organisms are from their common ancestor. We can kind of guess at this information based on fossils, but we also use a molecular clock. I can make assumptions about how much genes diverge over time. 5. Evolution and Adaptation Life must evolve. In this course, we consider the theory of evolution as an explanation and fact. Environments, abiotic and biotic, are always changing, so species have to adapt through evolution, or move, or die. Life evolves through genes. Genetic variation is inevitable, due to mutations that change DNA sequences. Replication of DNA is very error-prone. 4 other things can cause mutations, such as background radiation from living on the planet or other external forces - ex: nuclear accidents -. This variation can affect adaptation, reproduction, and survival, sometimes helpfully, sometimes harmfully. We know that life evolves because we see genetic similarity beyond functional necessity that is explainable only by genetic relationship. Ex: There is no functionally necessary reason that a child may physically resemble their parents; this is explained instead by genetic relationship. Summary  Life is defined by: Evolution - proven by genetic similarity beyond functional necessity - 1. Metabolism 2. growth/self movement - ish - 3. Selective barriers 4. responsiveness to stimuli 5. Reproduction 6. evolution and adaptation mutations 7. Order 8. Regulation Life is considered to be a complicated interaction or relationship between non-living things. Homeostasis: An organism's ability to maintain a different internal environment - with relatively low variation - compared to an external environment. Evolution is explained or proven by genetic similarity beyond functional necessity ○ This is inevitable due to biotic and abiotic environments changing, and mutations occur Chapter 1 - Retroactive Pre-Reading We recognize life mainly based on what living things do. More properties: What is previously included from the lecture ○ order - highly ordered structures ○ regulation - regulatory mechanisms to maintain a beneficial internal environment Biologists classify life into 3 domains: 1. Domain Bacteria ○ Fairly simple cells ○ Microscopic organisms 2. Domain Archaea ○ Fairly simple cells ○ Microscopic organisms ○ Often live in Earth's extreme environments - hot springs, etc. - 3. Domain Eukarya ○ Called Eukaryotes ○ More complex cells ○ 4 sub groups - kingdoms - ○ 4.1. Protists - Kingdom - Mostly single-cell organisms  Biologists still arguing Fall into multiple kingdoms Kingdom Plantae Produce their own food by photosynthesis Kingdom Fungi Diverse group Mostly decompose organic wastes and absorb the nutrients into their own cells Kingdom Animalia - 4 Animals - Obtain food by eating other organisms Not necessarily other animals - plants = organisms - Biologists classify life into an organizational hierarchy. Here it is, from biggest to smallest - complex to simple - : 1. Biosphere Most regions of land, bodies of water, lower atmosphere 2. Ecosystem All organisms AND abiotic details - physical components - with which life interacts in a given environment 3. Community All of the organisms in an ecosystem 4. Population A group of plants/creatures of the same species that live in a certain community 5. Organism An individual living thing - ex: single for - 6. Organs and organ systems Body parts that perform a specific function Ex: nervous system: brain, spinal cord, and nerves Has 2 or more tissue types 7. Tissue A group of cells that have a similar function working together Ex: a group of neurons that make up brain tissue 8. Cell A fundamental, structural and functional unit of life Composed of many parts  9. Organelle A membrane-enclosed functional structure in a cell Ex: the nucleus is an organelle that encloses a cell's DNA - genetic instructions - 10. Assemblies of macromolecules Macromolecules containing 10,000+ atoms; very large; are a DIN They are assembled into larger structures - ex: proteins - and take up the majority of a cell's dry mass - cells are largely water - 11. Molecules A chemical structure that consists of 2+ atoms Ex: a DNA helix To study basic and widespread processes of life, biologists often use model organisms. Good model organisms Short generation time Small Doesn't necessarily need to be useful to humans Ex: yeast cells ○ Has relevant cell characteristics that previous favorite doesn't - e. coli - ○ Humans are relatively closely related to yeast - cellular - Ex: fruit flies ○ 75% of genes that can cause disease in humans ○ Can score physical appearance without killing them; ○ They have fairly malleable DNA Ex: mice and cats ○ often used for neurobiology ○ Have physiological elements that humans have that flies don’t have Ex: Arabidopsis thaliana ○ Small genome ○ Short generation time ○ Good for plant biology Corn is also sometimes used - it’s annoying to use Summary: 3 life domains: Domain bacteria, Domain archaea, Domain eukarya Domain Eukarya has 4 Kingdoms ○ Protists - multiple Kingdoms - ○ Plantae - photosynthesis - ○ Fungi - decompose organic wastes + absorb nutrients from that -  ○ Animalia - eats other organisms - Life's hierarchy of organization: Biosphere, Ecosystem, Community, Population, Organism, Organs and organ systems, Tissue, Cell, Organelle, Assemblies of Macromolecules, Molecules Good model organisms represent processes Short generation time and are small ○ Often used - yeast cells - similar to human cells - , fruit flies - easy to determine phenotypes, malleable DNA, 75% of genes that cause disease in humans - , mice and rats - neurobiology - and arabidopis thaliana - plant biology - Lecture 2/3 - Start of ch. 8 - Genes are found inside the nucleus - the largest and darkest staining organelle - on chromosomes. Eukaryotes have characteristic numbers of chromosomes: often, the more complex the organism, the more chromosomes - but not always; sugar cane, for example, has more chromosomes than humans -. Chromosomes are about equally composed of DNA and proteins. One long DNA molecule Proteins maintain structure The DNA exists in a mass of long thin fibers - it usually exists in a mass of these chromatins. The genetic information on these chromosomes is called alleles. Two chromosomes with the same genetic functions are homologous pairs for the same gene in the same place, but not necessarily the same traits - alleles -. Humans have 46 chromosomes with 23 homologous pairs. They have, for example, two copies of chromosome 17, one inherited from the mother and one from the father. The same genetic will be at the same place - locus - on each chromosome - say the gene deciding whether freckles appear - , but it may not have the same alleles - genetic information -. For example, one chromosome may have the allele for yes freckles, and the other may have the allele for no freckles. These homologous chromosomes will be the same length and have the same banding pattern. The character is the genetic function - ex: flower color - and the trait is the specific allele - ex: purple -. Plants can tolerate unusual chromosome numbers; humans and animals rarely can, with some exceptions. Ex: Down syndrome is 3 copies of chromosome 21. Many other cases of unusual chromosome numbers will result in death. Mitosis and the cell cycle Mitosis is a type of cell division in which a cell divides to produce 2 genetically identical daughter cells - also identical to itself -. This is the process that, for example, skin cells use to replicate themselves to repair skin. It is one part of the cell cycle. You can divide the cell cycle into 2 phases: the interphase and the mitotic phase. The mitotic phase is BOTH the cytokinesis at mitosis, which overlap. Interphase G, first gap ○ The cells grow during this phase, and make proteins and organelles. ○ Some cells will stop dividing and adopt specialized jobs. ○ Not all cells will stay in Go forever - this can be helpful or harmful. Cancer comes from cells that divide after they are supposed to have stopped and drop these specialized jobs Since these cells divide and can occasionally split and go to different places in the body, tumors can spread cells can come out of Go for a good reason. some cells can, for example, sense damage to skin and produce a scab SI-DNA synthesis This is the stage where the chromosomes duplicate. This creates 2 sister chromatids, containing identical - duplicated - genetic information - alleles - at the same loci - place on the chromosome - held together by a centromere note: chromosomes are defined by the centromere so although they have been copied, there is still considered to be 46 chromosomes, but 96 Chromatido G2-second gap The cell makes sure that everything has been replicated and make sure that everything is ready for the mitotic process Mitotic phase 1. Prophase - chromatin fibers coil / pack and form microtubules mitotic spindles begin to attach to  2. Prometaphase - nuclear envelope breaks, microtubules reach for the chromosomes from opposite 3. Metaphase + mitotic spindle is fully formed, and the chromosomes line up on the metaphase plate - a concept - not physical, ex equator -. The mitotic spindles are attached and start to tug 4. Anaphase - the spindles pull each sister chromatid apart, and the centrosomes come apart. The spindle microtubules that are attached to other microtubules lengthen, elongating the cell. 5. Telophase - the cell keeps elongating, the chromatin fibers uncoil, a nuclear envelope develops around the chromosomes, and the mitotic spindle disappears. This is the end of mitosis. 6. Cytokinesis - the division of cytoplasm, occurs simultaneously with telophase. The two cells are completely separating into two daughter cells. In animal cells, a cleavage furrow forms and the cell drawstring in 2 different parts of the body and perform different functions. Cytokinesis is very different in plant cells - the walls don't split up to divide the cell. "Little bags" of cell wall material collect in the middle of the - cell plate - cell. This material will produce a cell wall in the middle of the expanded cell, officially dividing the cell. Because of this process, plant cells that have divided remain connected to each other by a cell wall. This does not happen in animal cells; they divide completely and can go to different parts of the body to perform different functions. Mitosis happens in growing unicellular organisms, embryonic cells in young animals, stem cells of mature animals, cells in the growing points of plants, injured tissue and cancer cells Summary: Chromosomes contain genetic information - called alleles - and are composed of chromatin - DNA + proteins - that contain these alleles and a centrsomes Homologues pairs - or homologs - are pairs of chromosomes found in the nucleus of the cell. They are found in the nucleus of the same information for the genetic functions, but can contain different traits - alleles - - often one of these will be paternal and one will be maternal A cell cycle containing mitosis is broken into 2 phases: Interphase and the mitotic phase Interphase: G, or Go - growth 1 - or - cell is no longer in the cell cycle -. S. - DNA replication - - sister chromatids - G2 - self check - Mitosis Mitotic phase - Mitosis + cytokinesis - - Pumatsol - Prophase - chromatin coils, microtubules grow · Prometaphase - bye bye nuclear envelope! Spindle microtubule hold hands or grab that chromatin · Metaphase- line up! Chromosomes at metaphase plate Anaphase - Yoinked. Chromosomes get pulled apart into the sister chromatins + microtubules push away from each other Telophase - chromatin uncoils, cell keeps on spliting Cytokinesis - division of the cytoplasm; for animals, cleavage furrows and byeee! For plants; keep holding hands at the cell wall Lecture 4 - Chapter 8 - Meiosis Meiosis is a reductional division Each daughter nucleus gets half the chromosomes Meiosis results in 4 daughter cells with 23 chromosomes Each daughter cell will be genetically different from the mother and any other gamete - in humans - ever created Meiosis is used for sexual life cycles, when fertilization causes a fusion of the nuclei of two parent cells. This process increases genetic variability in a species, and allows for evolution. Asexual reproduction doesn't do this, and so these species tend not to survive as long A homolog is one chromosome in a homologous pair. In Meiosis, the cell still goes through interphase before it starts Meiosis, meaning the chromosomes have already been duplicated 10 meiosis 1 before interphase Stages of Meiosis 1. Prophase 1 - homologs find each other, and the 2 sets of sister chromatids align and touch. The chromatids will then often trade segments, splitting of exactly the same place. This process is called crossing over, and it could happen anywhere, being largely random. This can happen usually 0-3 times for one particular homologos pair.  2. Metaphase 1 - the homology will line up, op, still paired together with one closest to each pole of the cell. Which side each particular chromosome ends up on is also random; you could have, for example, 7 from the father, and the reverse on the other side. These pairs will line up on the metaphase plate, and the spindle microtubules will attach to the chromosomes and each other, but NOT individual chromatids 3. Anaphase 1 - microtubules will separate homologs with the chromatids - that are likely no longer identical, due to crossing over - still attached to each other. The cell starts to lengthen 4. Telophase 1 and Cytokinesis - the cell splits into 2 new haploid cells. 5. Prophase 2 - There is no duplication before this phase! It starts with the already duplicated chromatids from Meiosis 1 6. Metaphase 2 - chromosomes line up on the metaphase plate, microtubules do their thing. 7. Anaphase 2 - microtubules yoink and stretch, sister chromatids separate. 8. Telophase 2 and Cytokinesis - haploid daughter cells form, each with - in humans - 23 chromosomes, with no homologous pairs. Sexual life cycles Typical animal and plant cells each have 2 chromosome sets - 2 homologues of each chromosome - ; the cells are diploid - 2n -. A chromosome set consists of 1 homologue for every chromosome that makes up that species - 23 for humans - ; all genetic functions are represented. Typical gametes - eggs and sperm - each have only one chromosome set, because of chromosome reduction in meiosis; these cells are haploid - 1n -. Sexual fertilization involving two 1n gametes produces a 2n fertilized egg, called a Zygote Meiosis results in genetic variability in the meiotic products, and therefore in a species with a sexual life cycle Some organisms will go through meiosis and then do mitosis on the meiotic products Sometimes these organisms will asexually reproduce, and sometimes they will sexually reproduce ○ think the pea plants ○ this is for plants - once animal cells have gone through meiosis, they won't divide anymore DNA replication During DNA replication, the strand of DNA comes apart, either AT or GC - in any order - The DNA strand is composed of complementary bases, as the proteins holding it together dissolve.  Once the DNA strand is pulled apart, the cell will fill in the blanks and put in the complementary base - 1/10,000 error rate -. The cell will proofread its work; this also has ~ 1/10,000 error rate DNA is used to create specific proteins Summary Meiosis starts with haploid - 2n - cells and finishes with 4 a haploid - In - cells - daughters - During this process, DNA replication occurs, but unlike in Mitosis, during meiosis 1 the best homologues separate into different cells with their duplicated sister chromatids. During meiosis 2, those chromatids separate. Meiosis also has crossing over, where those chromatids separate. Meiosis also has crossing over, where chromosomes will change arms. Prophase 1 - crossing over, homologues pair up Metaphase 1 - homologues line up on the metaphase plate - one close to one pole, vise versa Anaphase 1 - homologues get pulled apart Telophase 1 and cytokinesis - the cell splits into 2 haploid cells with 2 sister chromatids - no longer always identical - Prophase 2 - no chromosome duplication here! Metaphase 2 - chromatids get lined up on the metaphase plate Anaphase 2 - chromatids get pulled apart Telophase 2 and cytokinesis - cell splits resulting in 2 - 4 total - haploid daughter cells Animal cells will stop here; some plant cells will do mitosis on the post meiosis cells. When 2 of the products fertilize, the product is a diploid zygote. Meiosis creates genetic variability within a species and allows for evolution. During DNA replication, the strand gets pulled apart and the cell fills in the blanks with complementary bases; A and T or G and C go together. The cell will check its work. Each of these stages has about a 1/10,000 error rate. Genetics Genetics determines how hereditary information is passed through generations, which is contained in our DNA, which is packed into chromosomes. Evolution is the change in genetic structure over time: the organisms with the most genetic advantages would survive and breed. Many plants that are useful to us - ex: corn - were genetically developed by humans sometimes accidentally - to be more useful to us. Gregor Mendel was the first person to come up with a theoretical understanding of inheritance.