BIO1101 PBLsummary - bbnb PDF

Preview

Summary

bbnb...

Description

Zoé Ducarne

BIO 1101: PBL Summary LIVING THINGS, VIRUSES AND PRIONS Characteristics for being alive -

Order: highly organized structures, are built of cells (cells, tissues, organs, organ systems) Evolutionary adaptation: Populations of organisms evolve to produce individuals that are adapted to their specific environment. Pass their traits onto their offspring Homeostasis: ability to maintain constant internal conditions Growth and development: All organisms grow and develop following specific instructions coded for by their genes Response to environment: interaction with environment is shown by response to stimuli Reproduction: by duplicating their DNA, genes containing DNA are passed along to offspring Have a metabolism: use of a source of energy for metabolic activities (transport minerals/water and make or break down energy from those)

Viruses -

Structure o Nucleic acid genome surrounded by a protein coat, the capsid made of capsomeres, and sometimes an envelope made of phospholipids.

-

Alive or dead ? o Viruses cannot reproduce by themselves but need the host cell. And cannot maintain homeostasis, they cannot monitor changes. But, they do have DNA How it causes diseases 1. Virus binds to host cell via receptor molecule on the cell surface 2. Virus (or its genetic material) enters the cell 3. The viral genome is copied, and its genes are expressed to make viral protein 4. The new viral particles are assembled from genomes copies and viral proteins 5. Those new viral particles exit the cell and can infect other cells Reproduction Cycle-evolutive adaptaion o Lytic (where the virus actively replicates in a host cell) → the host-cell gets destroyed after a while o Lysogenic phase (where the viral DNA incorporates itself into the cell’s DNA and multiples whenever the cell multiplies) → the virus integrates into the cell.

-

-

Prions -

-

Structure o Prions are proteins, they cause neurodegenerative diseases. Prions are misfolded form of proteins present in the brain and when the prion gets to a cell containing the normal form of the protein, it converts the normal protein into a misfolded one. o So you can have chains. o Can withstand extreme conditions (heat/radiation)  are indestructible Alive or dead? o Prions are proteins, so no living organism and do not contain DNA. How it causes diseases o Prions when they are in the folded forms can form chains and interfere with normal cellular functions → can form symptoms of the disease. Making holes in the brain.

Prions vs Viruses -

Virus does have nucleic acid vs prion who do not Viruses are a lot smaller than prions. Mostly shorter incubation time virus vs long incubation time in prions

MACROMOLECULES AND THE ORIGIN OF LIFE Macromolecules -

Function

Macromolecule

Function

Example

Carbohydrates

Provide cells with quick/short term energy Structure for the cells

Glucose, sucrose, starch, cellulose, chitin

Lipids

Provide cells with long-term energy, make up biological membranes Steroids to faster regenerate the muscles (prevent inflammation) → hormones

Fats, phospholipids, waxes, oils, steroids

Proteins

Provide cell structure, send chem signals (hormones), speed up chem reactions, transportation, storage of amino acids, allows muscles to contract, defense system, allow for growth, regulates pH

Keratin, hormones, enzymes, antibodies

Nucleic acids

Store and pass on genetic information Regulation, transcription and translation

DNA, RNA

-

Structure

Proteins (polymers of amino acids)

Lipids Phospholipids:

Steroids: Nucleic acids (DNA and RNA; polymers of nucleotides)

Fats: Carbohydrates (polymers of sugars)

Glucose creation of glycogen, starch and cellulose with having different functions -

-

Protocells

Depends on the glycosidic bond. Starch: made up of glucose monomers that are joined by α 1-4 or α 1-6 glycosidic bonds, its function is storage. o Amylose: α 1-4 glycosidic bonds, o Amylopectin (branched polymer): either α 1-4 or α 1-6 glycosidic bonds. The α 1-4 is the same as for amylose and the α 1-6, a branch point is made. Cellulose: made up of glucose monomers that are linked by β 1-4 glycosidic bonds, its function is building material (cell walls) Glycogen: similar in structure to amylopectin but branches more frequently.

-

Initial structures during the origin of life which can show at least one property of life Structure: Consist of membrane (lipids) and RNA, are circular

From RNA to DNA and Ribozymes -

RNA: single stranded is unstable and easily damaged by enzymes How: by doubling the existing RNA molecule, and using deoxyribose sugar instead of ribose DNA: double stranded, much more stable form to pass genetic info Ribozyme: made of RNA, act like proteins, thus catalysts (Ribozymes are made of RNA and because ribozymes are catalysts, RNA is also one)

Origin of life -

-

Volcanoes o Miller-Urey experiment: stimulating earth early conditions (atmosphere, lightnings, etc.) they could create organic compounds and different types of amino acids Hydrothermal Vents & warm shallow oceans o First hypothesis: nitrogenous oxides, could have reacted with carbon dioxide from the vents o Second hypothesis: nitrogenous oxides and RNA when in contact can allow for the formation of life/molecules (either in oceans or shallow waters) o Nitrogenous oxides broken down by lightning o This also happens due to UV light and reactions with primitive rock (iron) in oceans, decreasing the concentration of nitrogen (by factor of 1000). o This doesn’t occur in shallow water (puddle rather than small lake) as the concentration of the nitrogenous oxide is higher (no primitive rock)

ATP, PHOTOSYNTHESIS AND CELLULAR RESPIRATION ATP -

How to get it: glucose is broken down during cellular respiration into ATP especially during oxidative phosphorylation). Organisms living near vents use energy escaping from hydrothermal vents to produce ATP. They can oxidize H2S from hydrothermal vents and use the energy released in this process to fix inorganic carbon from water into sugars that can then go under respiration.

Photosynthesis -

Happens in chloroplast Chemosynthesis: similar process, instead of using sunlight, it uses chemicals as a source of energy. Used by prokaryotes in hydrothermal vents. Chlorophylls absorb light energy which is converted into ATP and NADPH. Then, Clavin cycle use ATP and NADPH to fix CO2 (incorporate it into organic molecules) and produce

-

G3P (glyceraldehyde-3-phosphate, a 3-carbon sugar) which join up and produce glucose (C6H12O6) Light reactions: o Happens in thylakoid membrane (chloroplast) o In Photosystem II: electron is boosted up (so high energy) by light hitting the system and passed to an electron acceptor and replace by an electron from water. Systems splits H2O from which we get O2 o In Photosystem I: light hitting the system boosts up electron that was at lower energy after few passes between redox enzymes. o NADPH formation: the high energy electron coming from PSI id passed to NADP+ to make NADPH o ATP synthesis: the electron travels down electron transport chain, the released energy drives pumping H+ from stroma (low concentration) into the thylakoid space (high concentration). As H+ flow into the stroma they pass through ATP synthase, driving ATP production.

-

Calvin cycle: o Happens in stroma (space within chloroplast) o 1 CO2 enters the cycle but 3 are needed for 3 carbon sugars which can be turned into glucose. o Phase 1 (Carbon Fixation): CO2 combines with RuBP (5-carbon acceptor molecule) making 3-PGA (3-phosphoglyceric acid) o Phase 2 (Reduction): ATP and NADPH convert the 3-PGA into G3P (NADPH reduces a 3-carbon intermediate to make G3P) o Phase 3 (Regeneration): some G3P molecules make glucose and the rest are recycled to regenerate RuBP acceptor

-

In/Out, where o Light reactions  In: energy and H2O  Out: ATP, NADPH and O2

 Happens in thylakoid membrane (chloroplast) o Calvin Cycle  In: CO2, uses ATP and NADPH produced by light reaction  Out: glucose (C6H12O6) produced by G3P, ADP, NADP+  Happens in stroma (space within chloroplast)

Respiration A glucose molecule is gradually broken down into CO2 and H2O. Some ATP is produced in those reaction that transform glucose and later in oxidative phosphorylation. The process of oxidative phosphorylation is powered by electron movement through an electron transport chain. Those electrons are coming from the glucose and are shuttled to the electron transport chain by NAD+ and FAD (electron carriers) that become NADH and FADH2. - Oxygen allows production of a lot of ATP, if no oxygen electron transport chain (which produces atp) does not work bc no acceptor at the end. - Steps 1. Glycolysis o Happens in cytosol o 1 Glucose (6-carbon) gets converted into 2 pyruvate molecules (a 3-carbon molecule) o ATP is made o NAD+ is converted into NADH (electron carrier) 2. Pyruvate Oxidation o Happens in mitochondrion (mitochondrial matrix) o Pyruvate molecules are converted into a 2-carbon molecule to bound to acetyl coenzyme A (acetyl CoA) o CO2 and acetyl CoA is released o NADH is generated and released 3. Citric Acid Cycle o Happens in mitochondrion (mitochondrial matrix) o Acetyl CoA combines with 4-carbon molecule and goes through cycle of reaction o ATP, NADH and FADH2 (electron carriers) are produced with a bit of energy o CO2 is released 4. Oxidative Phosphorylation: o Happens in mitochondrion (inner membrane) o NADH and FADH2 deposit their electron in the electron transport chain (make them go back to NAD+ and FADH) o As electron move down the chain, energy is released and used to pump protons (H+) o Protons flow in the matrix through ATP synthase (water mils structure) making ATP o At the end of the electron transport chain, oxygen accepts electrons (because it is highly electronegative) and takes up protons to form water -

-

In/Out, where o Glycolysis:  In: Glucose

 Out: ATP, NADH (electron carrier), 2 pyruvate molecules  Happens in cytosol o Pyruvate Oxidation  In: 2 pyruvate molecules  Out: CO2 and acetyl CoA  Happens in mitochondrion o Citric Acid Cycle  In: Acetyl CoA  Out: CO2, ATP, NADH and FADH2  Happens in mitochondrion o Oxidative Phosphorylation:  In: NADH and FADH2  Out: H2O, ATP  Happens in mitochondrion

Fermentation - Fermentation = metabolic process that produces chemical changes in organic substrates through the action of enzymes - Happens when there is no O2, to produce ATP (less ATP produced than respiration, 2 vs 38) - Extracts energy from carbs - Begins in cytoplasm too

MITOSIS, MEIOSIS AND REPRODUCTION Mitosis Steps -

Prophase: o Nuclear membrane desegregates o Nucleolus disappears o Centrosomes migrate from each side of the former nucleus

-

-

-

o A microtubule spindle forms, linking the 2 centrosomes together o Chromatin is compacted in double chromosomes o Microtubules attach to the centromere of each double chromosome Metaphase: o Centromeres of each double chromosome aligns along an equatorial plane thanks to the elongation/shortening of the mitotic spindle Anaphase: o Microtubules shorten and lead to the separation in simple chromosomes Telophase: o Simple chromosomes decondense in chromatin o Mitotic spindle disappears o Nucleolus and nuclear envelop reform Cytokinesis o Cytoplasm and organelles are separated evenly in order to form daughter cells o Animal cells: actin and myosin create a contractile ring which separates the cells. o Plant cells: the cell wall allows the two cells to separate

Meiosis Steps -

-

-

-

-

-

-

Prophase I o Nuclear envelope and nucleolus disappear o Centrosomes arrange a meiotic spindle and move toward each pole o Homologous chromosomes pair up and form tetrads (4 chromatids) Metaphase I o Paired chromosomes align along the metaphase plate with one chromosome of each pair facing each pole Anaphase I o Microtubules pull homologous chromosomes to opposite poles o Chromosomes of each pair are separated Telophase I and Cytokinesis o Nuclear envelop and nucleolus reappears around chromosomes o Spindle disappears o Cytokinesis divides cytoplasm in 2 Prophase II o Nuclear envelope and nucleolus disappear again o Centrosomes arrange a meiotic spindle, this one has a perpendicular orientation when compared to meiosis I o Chromosomes condense Metaphase II o Chromosomes align along the metaphase plate Anaphase II o Chromatids are separated and move toward opposing poles Telophase II and Cytokinesis o Chromatids are located at each pole and decondense into chromatin o Nuclear envelop and nucleolus reappears

o Spindle disappears o Cytokinesis occurs

Asexual reproduction -

-

Major method: o Binary fission: single parent cell splits into 2 identical daughter cells of the same size. Often in bacteria o Fragmentation: parent organism breaks into fragments. Each fragment develops into a new organism o Budding: parent cell forms a bud, a localized mass of mitotically dividing cells. The bud grows and develops while staying attached to the parent cell. When it is fully developed, it detaches from the parent cell and form a new organism o Parthenogenesis: egg develops into a complete individual without being fertilized. o Single celled eukaryotic organisms can reproduce asexually by mitotic cell division Only need 1 parent, so do not spend time on searching for a mate, energy efficient on doing it by yourself, no fertilization time. Higher chance that there will be offspring. Genetic variations can only arise as mutation, a non-beneficial or harmful trait will therefore be passed on over and over if mutations occur. Asexual reproduction can be “safer” depending on the environment, if parent is thriving etc.

Life Cycles Types of sexual life cycles: - Diploid dominant: have multicellular diploid stage as the most important life stage. Haploid cells are the gametes - Alternation of generations: both the haploid and the diploid stages are multicellular o Diploid multicellular stage = sporophytes o Haploid multicellular stage = spores (produced by meiosis in sporophytes) grow by mitosis into gametophytes (produce gametes by mitosis) - Haploid dominant: have multicellular haploid stage as the most important life stage. Diploid cells are zygotes

Genetic Variations Different mechanisms: - Crossing over: o Happens during prophase I of meiosis I o Is the exchange of genetic material between non sister chromatids of homologous chromosomes  new combination of genes on each chromosome - Independent assortment: o homologous chromosomes are randomly distributed to daughter cells during meiotic metaphase (2 possible orientation at the metaphase plate) o hence, gametes have unique combination of chromosomes o possible number of alignments = 2n - Random fertilization: o random fertilization of a gamete from female using gamete from male o sperm cell has 2n chromosome combination fertilizes with as an egg with also 2n chromosome combination o human 8 million 8 million  64 trillion combination

EVOLUTIONARY FORCES AND FITNESS Evolutionary Forces 4 different types: - Natural selection: individuals with certain inherited traits survive and reproduce at higher rates because of those traits. o Can cause adaptive evolution: traits that enhance survival or reproduction tend to increase in frequency o Natural selection is dependent on the environment, adaptations in one environment may not be beneficial in others. o Different types of selection:  Directional: moving along a scale of variation toward one endOccurs when conditions favor individuals exhibiting one extreme phenotypic range, shift of population phenotypic curve  Disruptive: there is benefit on 2 extremes of a range of phenotype, those are both selected but the intermediate one are not as successful Occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotype  Stabilizing: when an intermediate is the most beneficial and we select around that middle phenotype Acts against both extreme phenotypes and favor intermediate one, reducing variations - Sexual selection: individuals with certain inherited characteristics are more likely to obtain mate o Characteristics do not have to be beneficial o Intrasexual: members of the same sex compete for mates o Intersexual: individuals of one sex are “picky” in their choice of mate (peacock) - Genetic drif: fluctuation of allele frequencies due to chance events o More important in small populations o Founder effect: few individuals start a new population (few members of a population blown by storm on a new island) o Bottleneck effect: sudden reduction in population size (storm, disease) - Gene flow: transfer of alleles into or out of a population due to o Movement of fertile individuals (animals) o Movement of gametes due to pollen (plants)

Random events in environment -

Fitness

Storms, disease, geological phenomenons resulting in a bottleneck effect (individuals would be killed by storm) or founder effect (individuals become isolated) Mutation Temperature change, nutrients not available or huge amount available

-

How well a species is able to reproduce in its environment and how successful an organism has been at passing on its genes. 2 ways to measure of fitness: o Absolute fitness: expressed as the total number of gene copies transmitted to the next generation or the total number of surviving offspring that an individual produces during its lifetime o Relative fitness: where reproductive rate (of genotype or phenotype) is relative to the maximum reproductive rate (of other genotypes or phenotypes) in a given population

Evolution does not create perfect organisms 4 constraints: - There are trade-offs, compromises within adaptation, for example structural reinforcement in human led to compromise for agility and makes us prone to torn of ligaments etc. - Populations can only evolve with the present genetics, new alleles do not emerge on demand, and therefore natural selection favors the best current allele among the others already present in the population. - Chance, natural selection and the environment interact so if some random events happens moving the population to a new environment, the population will have to adapt to this new environment, and this will be done with natural selection - Evolution is limited by historical constraints, evolution uses the existing structures, so the ancestral anatomy is taken into account, and adapts them the current situation rather than starting to build a brand-new structure....