Cellular Energetics

Unit 3: Cellular Energetics Chapter 8: An Introduction of Metabolism - Metabolism: totality of an organism’s chemical reactions o Rises from orderly reactions between molecules Metabolic Pathway: begins with a specific molecule which is altered in a series of defines steps, resulting in certain products Chapter 10: Photosynthesis - - - - Photosynthesis: capturing energy from the sun and converting it to chemical energy that is stored in sugar and other organic molecules Autotrophs: “self-feeders” Stoma / Stomata: microscopic pores in the leaf where carbon dioxide enters and oxygen exits Stroma: dense fluid in the chloroplast which is surrounded by two membranes Thylakoids: a third membrane system made of sacs that are suspended in the stroma and segregate the stroma from the thylakoid space in these sacks o Singularly called grana Chlorophyll: green pigment that gives leaves their color and resides in the thylakoid membrane 6 C O2 +6 H 2 O → C6 H 12 O6 +6 O2 Photosynthesis is endergonic Light Reactions: first step of photosynthesis o Convert solar energy to chemical energy o Splitting water provides a source of electrons and protons as a by-product  NADP+ is an acceptor of these o Light reactions use solar energy to reduce NADP+ to NADPH by adding a pair of electrons and H+ o Photophosphorylation: light reactions generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP o Ultimately produces NADPH (source of electrons) and ATP, not sugar Calvin Cycle o Carbon Fixation: incorporation of carbon into organic compounds  Incorporates C O2 o Reduces C O2 to carbohydrate by adding electrons from NADPH  Also required ATP o Also known as dark reactions Autotrophs have a variety of pigments to maximize light absorptions When light goes in the chlorophyll, the electron is excited and becomes extremely unstable A photosystem is made of reaction-center complexes surrounded by several light-harvesting complexes, which each have various pigment molecules o Light energy is transferred from pigment to pigment is taken by the primary electron acceptor o Photosystem II and Photosystem I o Electron transport chain is embedded in the thylakoid membrane of the chloroplast Electron Transport Chain 1. PS II electrons are excited and is transferred to electron acceptor 2. Enzyme splits water to 2H+ ions and an electron (replaced the electron that was transferred) 3. H+ ions are release into the thylakoid space 4. Photoexcited electrons travel to PS I 5. Exergonic “fall” of electrons to a lower energy level provides energy for ATP synthesis o As electrons pass through the cytochrome complex, H+ keeps being pumped to thylakoid space, contributing to the proton gradient 6. Light harvesting complex pigments transfer light to PS I and the photoexcited electron is transferred to PS I’s primary electron acceptor 7. Electrons are passed down a second electron transport chain through ferredoxin (Fd) 8. NADP+ catalyzes the transfer of electrons from Fd to NADP+ to make NADPH - CAM (crassulacean acid metabolism) Plants have photosynthetic adaptions to arid conditions o Succulent (water-storing) plants o Open stomata in the night and close them in the day Chapter 40: Basic Principles of Animal Form and Function - - - - - - - - Homeostasis: “steady state” referring to the maintenance of internal balance o Constant internal environment, even when the external environment changes significantly Negative Feedback: a control mechanism that reduces, or “damps,” the stimulus o Key in maintaining homeostasis o Ex: when exercising, the body temperature increases  nervous system triggers sweating  evaporation of moisture cools body Positive Feedback: control mechanism that amplifies the stimulus o Not a major role in homeostasis in animals o Helps drive processes to completion o Ex: contractions during childbirth Thermoregulation: process by which animals maintain their body temperature within a normal range o Body temperature outside normal range can decrease efficiency of enzymatic reactions, alter fluidity of cellular membranes, and affect other chemical process with potentially fatal results Endothermic: warmed mostly by heat generated by metabolism o Humans, mammals, birds o Can maintain a stable body temperature even with large external fluctuations Ectothermic: gain most of their heat from external sources o Not mutually exclusive with endothermy  Bird may sit in the sunlight to warm up Insulation reduces overall heat exchange between the body and environment Circulatory systems proved a route for heat flow between interior and exterior body o Vasodilation: widening of superficial blood vessels to warm the skin o Vasoconstriction: reduces blood flow and heat transfer my decreasing the diameter of superficial vessels Countercurrent Exchange: transfer of heat between fluids flowing in opposite directions Evaporative heat loss cools down the body because water absorbs considerable heat (high specific heat capacity) when it evaporates Behavioral Responses: seemingly simple ways to react to changes in homeostasis o Endo and ectotherms o May go towards heat surface when cold or bath when hot Adjusting metabolic heat production o Thermogenesis: vary heat production to match changing rates of heat loss Bioenergetics: overall flow and transformation of energy that decides its nutritional needs - - Chemical energy is used for growth, repair, activity, and reproduction Metabolic Rate: sum of all the energy an animals uses in a given time interval o Can be changed o Measured in joules, calories, or kilocalories o Measured by  Monitoring the rate of heat loss with a calorimeter  Amount of oxygen consumed or carbon dioxide produced  Rate of food consumption (for long term) and energy lost in waste products Body mass and metabolic rate is constant Unit 4: Cell Communication and Cell Cycle Chapter 11: Cell Communication Chapter 12: Cell Cycle - - - The continuity of life is based on reproduction from the cell cycle o Reproduction for prokaryotes and unicellular eukaryotes o Tissue renewal and growth and development for larger organisms  Ex: dividing cells in bone marrow to make new blood cells Cell Cycle: the life of a cell from the time it is first formed during division of a parent cell until its own division into two daughter cells o Passing identical information to offspring o Major role in cancer development Genome: genetic information o Really long naturally so it needs to condense before splitting Chromosomes: DNA is packaged into these structures before cell replication Chromatin: entire complex of protein and DNA that is building blocks of chromosomes Gametes: sex cells that have half as many chromosomes (haploid) Sister Chromatids: the duplicated chromosomes that are joined at the center by centromeres o Later separate into each of the daughter cells Mitosis: division of genetic material in the nucleus o Followed by cytokinesis: division of cytoplasm Centrosome: a subcellular region containing material that functions throughout the cell cycle to organize the cell’s microtubules Cell Cycle Phases 1. Interphase o G1 Phase o S Phase (synthesis)  DNA duplication o G2 Phase  Nuclear envelope encloses that nucleus  DNA is not condensed yet o Longest part of the cell cycle 2. M Phase o Mitosis  Prophase  Chromatin fibers begin to condense a little bit  Nucleoli disappears  Sister chromatids join at the centromere  Mitotic spindle begins to form in the cytoplasm o Aster: radial array of microtubules o Made of centrosomes and microtubules  Centrosomes move away from each other, propelled by the lengthening microtubules  Prometaphase  Chromosomes condense  Nuclear envelope fragments  Microtubules and kinetochores (kinetochore complex) Metaphase  Centrosomes are at opposite sides of the cell  Metaphase Plate: a plane that is equidistant from the mitotic spindle’s two poles o Chromosomes arrive here  Anaphase  Shortest stage  Cohesin proteins  suddenly pull the sister chromatids apart  At the end, both parts have equal and identical chromosomes  Telophase  2 daughter nuclei appear and the nuclear envelope reassembles  Nucleoli reappear  PMAT – Pet My Adorable Tiger o Cytokinesis  Cleavage furrow pinches the cell into 2 parts  Groove near the old metaphase plate  Splits the cytoplasm in half  separate into two different cells  Plants use cell plates  Unit 5: Heredity Chapter 13: Meiosis and Sexual Life Cycles - - - - - - - - Heredity: transmission of traits from one generation to the next o Inheritance Variation: sons and daughters are not identical copies of either parent or siblings Genetics: scientific study of heredity and variation Genes: parents endow their offspring with this coded information o Hereditary units DNA: polymer of four different nucleotides o Communicated in the form of letters o Often copied before transmission, so that the genes can be passed from parent to offspring Gametes: vehicles that transmit genes from one generation to the next o 23 chromosomes (haploid) Except for small amount of DNA in mitochondria and chloroplast, the DNA of a eukaryotic cell is packaged in chromosomes in the nucleus Somatic Cells: all cells of the body except the gametes and their precursors o 46 chromosomes (diploid) Asexual Reproduction: a single individual passes copies of all its genes to its offspring without the fusion of gametes o Mitosis o DNA is copied and allocated equally to two daughter cells o Clone: a group of genetically identical individuals Sexual Reproduction: two parents give rise to offspring that have unique combinations of genes inherited from the two parents o Meiosis o Genetic variation Life Cycle: generation-to-generation sequence of stages in the reproductive history of an organism, from conception to production of its own offspring Karyotypes: images of chromosomes arranged in pairs, starting with the longest chromosomes o Homologous Chromosomes / Homologs: two chromosomes that have the same length with a centromere Sex Chromosomes: X and Y chromosomes o Autosomes: all other chromosomes Diploid Cell: diploid or “double” number of chromosomes o Abbreviated as 2n o Somatic cells Haploid Cells: haploid or “single” number of chromosomes o Abbreviated as n o Gametes Organisms that do meiosis have a unique number of diploid and haploid chromosomes Fertilization: union of gametes, culminated in the fusion of their nuclei o Zygote: resulting fertilized egg  Mitosis of the zygote and all its descendant cells generates all the somatic cells of the body Meiosis: cell division that involves gamete formation o Fertilization restores diploid number of chromosomes o Sister Chromatids: two copies of one chromosome  Their association is called sister chromatid cohesion 1. Prophase I: centrosomes move, spindles form, and the nuclear envelope brakes down  Crossing Over: DNA molecules of non-sister chromatids are broken and are rejoined together o Synpasis 2. Metaphase I: pairs of homologous chromosomes are arranged at the metaphase plate  Independent Assortment: random orientation of pairs of homologous chromosomes at the metaphase plate o Produces genetic diversity  Two possible orientation produces 50% change of getting mother or father chromosomes 3. Anaphase I: separate sister chromatids  Spindle apparatus moves homologs to opposite poles 4. Telophase I: cleavage furrow forms to start splitting into two cells  Begins with each half of the cell having a complete haploid set of duplicated chromosomes 5. Cytokinesis: division of cytoplasm to form two haploid daughter cells 6. Prophase II: spindle apparatus forms and chromosomes (with two chromatids) move to the metaphase II plate 7. Metaphase II: chromosomes are positioned at the metaphase plate  Sister chromatids of each chromosomes are not genetically identical because of crossing over 8. Anaphase II: sister chromatids separate and go to opposite poles through spindle fibers 9. Telophase II and Cytokinesis: nuclei form, chromosomes decondense, cytoplasm is split o Results in four genetically distinct haploid daughter cells o Recombinant Chromosomes: individual chromosomes that carry genes derived from two parents - Alteration of Generations: plants and some species of algae exhibit both diploid and haploid stages that are multicellular Other forms of asexual reproduction: o Fission: separation of parent organism into two individuals of approximately equal size o Asexual reproduction can be a two step process 1. Fragmentation: breaking of the body into several pieces a. Regeneration: regrowth of the lost body parts o Pathogenesis: egg develops without being fertilized  Happens in invertebrates such as wasps and ants Chapter 12: Cell Cycle - - - Cell Division: continuity of life based on the reproduction of cells o Passing identical information to offspring o Major role in cancer development The continuity of life is based on reproduction from the cell cycle o Reproduction for prokaryotes and unicellular eukaryotes o Tissue renewal and growth and development for larger organisms  Ex: dividing cells in bone marrow to make new blood cells Genome: genetic information o Really long naturally so it needs to condense before splitting Chromosomes: DNA is packaged into these structures before cell replication Chromatin: entire complex of protein and DNA that is building blocks of chromosomes Gametes: sex cells that have half as many chromosomes (haploid) Sister Chromatids: the duplicated chromosomes that are joined at the center by centromeres o Later separate into each of the daughter cells Mitosis: division of genetic material in the nucleus o Followed by cytokinesis: division of cytoplasm Centrosome: a subcellular region containing material that functions throughout the cell cycle to organize the cell’s microtubules Cell Cycle Phases 3. Interphase o G1 Phase o S Phase (synthesis)  DNA duplication o G2 Phase  Nuclear envelope encloses that nucleus  DNA is not condensed yet o Longest part of the cell cycle 4. M Phase o Mitosis  Prophase  Chromatin fibers begin to condense a little bit  Nucleoli disappears  Sister chromatids join at the centromere  Mitotic spindle begins to form in the cytoplasm o Aster: radial array of microtubules o Made of centrosomes and microtubules  Centrosomes move away from each other, propelled by the lengthening microtubules  Prometaphase  Chromosomes condense  Nuclear envelope fragments  Microtubules and kinetochores (kinetochore complex)  - - Metaphase  Centrosomes are at opposite sides of the cell  Metaphase Plate: a plane that is equidistant from the mitotic spindle’s two poles o Chromosomes arrive here  Anaphase  Shortest stage  Cohesin proteins  suddenly pull the sister chromatids apart  At the end, both parts have equal and identical chromosomes  Telophase  2 daughter nuclei appear and the nuclear envelope reassembles  Nucleoli reappear  PMAT – Pet My Adorable Tiger o Cytokinesis  Cleavage furrow pinches the cell into 2 parts  Groove near the old metaphase plate  Splits the cytoplasm in half  separate into two different cells  Plants use cell plates Kinetochore: structure made up of proteins that have assembled on specific sections of DNA at each centromere Metaphase Plate: imaginary plate rather than an actual cellular structure where the genetic information lines up Some specialized cells such as fully formed nerve and muscle cells do not divide in mature humans Cell Control System: cyclically operating set of molecules in the cell that both triggers and coordinates key events in the cell cycle o Checkpoint: control point in the cell cycle where stop and go-ahead signals can regulate the cycle  Most important ones are found in G1, G2, and M phases o Fluctuations in molecules (protein kinases and cyclins) and cell activity pace the cell cycle  Cyclin: protein that gets its name from its cyclically fluctuating concentration in the cell that activates kinases  Cyclin – Dependent Kinases (Cdks): activity of these rise and fall depending on the concentration of its cyclin partner Density – Dependent Inhibition: crowded cells stop dividing Anchorage Dependence: to divide, must be attacked to substratum such as a culture flask or extracellular matrix of a tissue Chapter 14: Mendel and the Gene Idea - - - Gregor Mendel chose to work with pea plants 1. Many varieties – heritable features that vary among individuals 2. Short generation time and large number of offspring from each mating Each pea plant has pollen-producing organs (stamens) and an egg-bearing organ (carpel) o Normally, pollen grains from the stamen land on the carpel of the same flower and fertilization occurs o Mendel removed stamens from the flower and pollinated them so that he could control their reproduction Mendel chose to track characters that appeared only in two distinct, alternative forms (i.e. purple or white flower color) - - - True – Breeding: over many generations, the plant only produced the same variety as the parent plant Hybridization: mating, or crossing, of two true-breeding varieties o Mendel initially crossed plants with purple and white flowers with each other P Generation: true – breeding generation F1 Generation: hybrid offspring (first generation) o All had purple flowers F2 Generation: offspring produced when the F1 generation self-pollinates (second generation) Law of Segregation: two alleles for a heritable character segregate (separate from each other) during gamete formation and end up in different gametes Alternative versions of genes account for variations in inherited characters (i.e. alleles) o Know dominant vs. recessive allele Punnett Square: diagrammatic device for predicting the allele composition of offspring from a cross between individuals of known genetic makeup o Monohybrid: heterozygous for the one particular character being following in the cross o Dihybrid: individuals heterozygous for two characters being following in the cross Law of Independent Assortment: two or more genes assort independent – each pair of alleles segregates independently of each other pair of alleles – during gamete formation o Worked because Mendel only studied genes located on different chromosomes Complete Dominance: the dominant trait completely covers the recessive one Incomplete Dominance: when the recessive trait is not completely covered by the dominant one (i.e. red and white flowers make pink offspring) Codominance: two alleles each affect the phenotype in separate, distinguishable ways Pedigree: a family tree describing the traits of parents and children across multiple generations Carriers: heterozygotes that may transmit the recessive allele to their offspring Some diseases follow Mendelian inheritance o Sick-Cell Disease: caused by the substitution of a single amino acid in the hemoglobin protein of red blood cells  Autosomal recessive disorder  When the oxygen content of the blood is low, the sickle-cell hemoglobin proteins aggregate into long fibers that deform the red blood cells o Huntington’s Disease  Autosomal dominant disorder  Causes progressive break down of nerve cells in the brain that results in movement, cognitive, and psychiatric disorders