Results for "payoff phase"

BIOC 503 - Glycolysis

Glycolysis: Prep phase, payoff phase, fermentation, pyruvate dehydrogenase, TCA

Concept 7.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate There are 2 important roles of glycolysis! 1. To produce energy molecules for the cell to use in its life processes. 2. To produce pyruvate, which can feed the citric acid cycle in the mitochondria of eukaryotes and the cytosol of prokaryotes and ultimately into the electron transport chain where most of the ATP in cellular respiration is produced. o In glycolysis (which occurs in the cytosol of all cells with or without oxygen), the degradation of glucose begins as it is broken down into 2 pyruvate molecules. The six-carbon glucose molecule is split into 2 three-carbon sugars through a long series of enzymatically controlled steps. o In the course of glycolysis, there is an ATP-consuming phase Energy Investment) and an ATP-producing phase (Energy Payoff). In the investment phase, 2 molecules of ATP are consumed which helps destabilize glucose and make it more reactive. Later in the payoff phase 4 ATP molecules are produced resulting in a net gain of 2 ATP molecules during glycolysis. In addition to a net gain of 2 ATP molecules 2 NADH s are produced which will be utilized later in the electron transport system. o Most of the potential energy of the glucose molecule remains in the two produced pyruvate molecules. If oxygen is present these molecules will be further degraded during the "grooming of pyruvate" (pyruvate oxidation) and the citric acid cycle. • It is important to note that the staring material for the Citric Acid Cycle is produced during glycolysis!!!! EVOLUTION CONNECTION It is presently theorized that glycolysis was the first ATP-producing metabolic pathway to evolve. There are 3 convincing reasons as to why this theory is probably true! 1. Long ago, Earth's atmosphere contained almost no oxygen, and only relatively recently have the current atmospheric levels of gases come to be what they are. Glycolysis does not require oxygen, so it is possible that prokaryotes (which evolved before eukaryotes) used this method for making ATP. 1. Glycolysis is a very common method for making ATP; in fact, almost all living organisms use it. This commonality implies that it originated very early in the evolution of metabolic pathways. 2. Glycolysis takes place in the cytosol of all cells not in an organelle Prokaryotic cells, which evolved first, are much simpler than eukaryotic cells, and they contain no membrane-bound organelles. Therefore, if glycolysis were to take place in an early prokaryotic cell, it would have to evolve such that it was capable of taking place in the cytosol-for instance, it would have to evolve such that it did not rely on a specialized membrane in order to function.

Payoff Phase

1.3 Macro Intro Breaking a bond = hydrolysis Build/make a bond = remove water, dehydration synthesis 1.4 Macros Nucleic Acids DNA and RNA Made from nucleotides A, T, C, G, U Proteins Amino acids Polypeptide To make it into a protein you need to fold and modify Carbs Monosaccharides Ex. glucose Polysaccharides Ex. starch, cellulose, glycogen, chitin Lipids nonpolar Ex. phospholipids Saturated (butter) vs unsaturated (oil) 1.5 Macros structure + function Uses covalent bonds between nucleotides Main structure want it to be covalent bond so its strong Bases use hydrogen bonds DNA is antiparallel, equally spaced read in opposite directions Protein Primary - Amino acids Secondary - Pleats and coils (hydrogen bonding) Tertiary - Interactions between the R-groups (unique shapes) Quaternary - 2 or more chains (any bond) Carbs Chains of sugars using covalent bonds 1.6 Nucleic Acids DNA Deoxyribose sugar T Double stranded RNA Ribose sugar U Single stranded Common Both use nucleotides A, G, C U2 Cells Organelles Ribosomes = protein synthesis Found on rough ER or free Show common ancestry Endoplasmic Reticulum Rough = ribosomes Smooth = makes lipids, detox Golgi complex Protein trafficking Packaging and transport of proteins mitochondria Site of cellular respiration, ATP production Double membrane Own DNA circular DNA Chloroplast Site of photosynthesis Own circular DNA Lysosome Hydrolytic enzymes Apoptosis Vacuole Large in plants Small in animal cells 2.3 Cell Size Small cells Inc surface area to volume ratio More efficient Better for transportation, elimination of waste, heat, exchanges, etc 2.4 Plasma Membrane Small and nonpolar can pass through easily (oxygen and carbon dioxide) 2.5 Membrane Permeability Selectively permeable Transport proteins needed for larger polar molecules Cell wall - plants, fungi, and prokaryotes Provides extra support and protection 2.6 Transport Passive transport (high to low) Does Not require any energy Diffusion Osmosis Facilitated diffusion (uses proteins) Active transport (low to high) Require energy Exocytosis Moving things in or out Endocytosis 2.7 Facilitated diffusion Uses integral proteins Ex. aquaporins, ion channels, neurons Proteins also used for active transport 3.6 Cellular Respiration Glycolysis Within the cytoplasm Evidence of common ancestry because all organisms go through glycolysis Glucose to 2 pyruvates Energy investment phase and energy payoff phase Get pyruvate, ATP, and NADH Fermentation (ONLY IF NO OXYGEN) To reset everything Takes NADH and turns it back to NAD+ to keep running glycolysis Grooming Phase Modify and turn it into Acetyl CoA Kreb Cycle With in the matrix Making electron carriers (NADH and FADH2) Inner mitochondrial membrane Where the electron transport chain takes place 3.7 Fitness Max offspring Variation can increase fitness Unit 4 Cell Communications 4.1 Signal Transduction Pathway Autocrine (signal yourself) Paracrine (next to you) Endocrine (far from you) 4.2 Signal Transduction Pathway intro Reception → transduction → response Reception: ligand attacks to the receptor The process by which a cell detects a signal in the environment. Ex. ligand binds to G protein which activates Transduction: phosphorylation cascade and amplifies signal The process of activating a series of proteins inside the cell from the cell membrane. Response: The change in behavior that occurs in the cell as a result of the signal. Second messenger - first is ligand, second messenger is for amplification (cAMP - each can have their own phosphorylation cascades) 4.3 STP Responses Turn gene off/on Apoptosis Cell growth start/stop 4.4 changes to STP Mutations (respond too much or too little to the signal molecule attacking) Chemical can release that can interfere with your STP resulting with death 4,5 Feedback Respond to changes (homeostasis) Negative (reverse change) Positive (increasing the change) 4.6 / 4.7 Cell Cycle/ Regulation G1 - growth G1 checkpoint (determine if you go to S phase or to G0 non dividing state) S - DNA replication G2 - organelle replication and growth G2 checkpoint - make sure the cell is ready for division M phase - Mitosis PMAT Prophase - nucleus disappears Metaphase - lined up at the equator Anaphase - replicated chromosomes are split Telophase - move to opposite ends M-phase checkpoint - checks to make sure division is correct Cytokinesis - final split into 2 Cyclin increases during S and peaks at M Cdk binds with cyclin to produce mpf Level of cyclins lets cell know where it’s supposed to be Tells your cell you are at your full maturity ready to produce Unit 5 Heredity 5.1 / 5.2 Meiosis Increases genetic variation Crossing over (Prophase 1) Reduction division haploid (half the amount of genetic information) Random fertilization Nondisjunction (meiosis 1 all 4 cells are irregular / meiosis 2 half the cells are irregular) Independent Assortment Increases genetic diversity 5.3 Mendelian Genetics A = dominant allele a = recessive allele Genotype - combination of letters (AA, Aa, aa) Phenotype = looks Law of Segregation - Aa → A / a Law of Independent Assortment (Aa Bb → AB, Ab, aB, ab) Sex Linked Located on a sex chromosome Usually X Sex linked recessive is more common in males because they only have one X Sex linked dominant both can inherit easily Incomplete dominance - blending Codominance - both alleles expressed 5.5 Environmental Effects Ex. weather, pH of soil 5.6 Chromosomal Inheritance Mutation → inherited Some have no effect, negative effect, neutral effect, 6.1 Gene Expression and Regulation 6.1 DNA Double stranded Deoxyribose T RNA Ribose Single stranded U 6.2 Replication (S-Phase) 5’ → 3’ Ligase - binds the new bases together Helicase - unwinds the DNA DNA poly - put down the new bases Primase - makes primer Topoisomerase - stops DNA from getting overwind Leading - able to all go in one go Lagging - many primers and okazaki fragments 6.3 Transcription and Processing Nucleus RNA poly makes primary transcript (pre mRNA) from DNA Template strand is the one the DNA is using to build Non template strand one not being used RNA processing Introns are removed Exons are put together Add cap and tail for protection Alternative splicing 6.4 Translation Ribosome Reverse Transcriptase retroviruses Ex. HIV RNA genomes use reverse transcriptase to make DNA from RNA 6.5 Regulation of Gene Expression Signal to unpack the gene Transcribed (transcription factors differ by cells and allows different gens to turn on) RNA editing Translation Polypeptide folding All need to go correctly or else the gene wont be expressed Acetylation of histones - adding acetyl group causes the DNA to be more loose making it easier to read Methylation of histones - adding methyl groups to the DNA causes it to be tighter and harder to read Enhancers - enhances transcription and causes it to occur more often Activators - dont bind to RNA poly it binds to the enhancer Depends of which genes and stage of development Epigenetics - one gene controls another gene Inducible Operon - usually off Repressor is bound to operon and lactose inactivates Repressible Operon - usually on Repressor is usually inactive, trp activates repressor 6.6 Gene Expression and Cell Specialization Promoter region (TATA box) alerts RNA poly that its a promoter region and where to attach Negative regulation - blocks promoter so RNA poly cant attach small RNA - can turn certain genes off 6.7 Mutations Increase normal gene function Decrease normal gene function Can lead to new phenotypes Cancer can be due to overproduction of growth factors, hyperactive proteins (requires many mutations Can have positive, negative, or no effect Causes of mutation Exposures Random Errors in DNA replication Increase or decrease in chromosome number Prokaryotes Transformation - pick up random DNA Transduction - virus accidentally is filled with bacterial DNA Conjunction - mating bridge/sex pilus 6.8 Biotechnology Electrophoresis - separates DNA by charge and size PCR - artificial DNA replication, increases amount of DNA sample Transformation - you make the bacteria take up a gene you're interested in Unit 7 7.1 Natural Selection natural / selective pressures decide survival Reproductive fitness (max out your kids) 7.2 Natural Selection Acts on phenotypes which can affect genotype Preferring brown fur over white decreases white fur allele frequency Environmental changes → selective pressures 7.3 Artificial Selection Humans select (ex. Dogs, livestock, etc) Convergent evolution - not closely related but because of similar environments you look alike Divergent - had a recent common ancestor but you started becoming separate Niche partitioning - choosing separate niches so you dont have to compete with others 7.4 Population Genetics Mutation - variety and evolution Genetic drift - random event that alters the gene pool Bottleneck effect - an event causes a large part of the population to die off and the remaining left repopulate with a different gene pool Founder effect - the og are there but some leave/get separated 7.5 Hardy Weinburg Large population No natural selection Random mating No mutation No gene flow P+q = 1 p2 + 2pq +q2 = 1 (AA) + (Aa) + (aa) = 1 7.6 Evidence of Evolution Fossils DNA (molecular homologies) Anatomy Vestigial structure (things we dont need anymore) (evidence of common ancestry) Biogeography (species are found all around the world)(kangaroos, genetic code, glycolysis) 7.7 Common Ancestry All Eukaryotes Membrane bound organelles Linear DNA and chromosomes Genes with introns 7.8 Continuing Evolution Genomic changes over time Continuous changes in fossils Evolution of antibiotic resistance Disease evolution 7.9 Phylogeny / Cladistics Phylogeny = included time Cladograms = just traits Shared characters Derived characters Molecular (DNA, proteins, amino acids) are more accurate than characteristics Parsimony - the one with the fewer events on it, the frewer you have the more likely it is 7.10 Speciesation Pre-zygotic Mechanical - parts dont match Gametic - egg doesnt match Geographical - dont live in the same place Temporal - ready to mate at different times Behavioral - specific type of mating display is not there Post-zygotic Hybrid sterility - the hybrid made is healthy but they cannot have children (mule) Hybrid breakdowns - the hybirds are okay but after a generation or two they cannot produce anymore Hybrid inviability - hybrid is produced but cannot survive long enough to reproduce Sympatric New species arrises in the original location Gradualism - slow steady evolution Allopstric Separation leads to speciation Punctuated - long periods of evolution with no change then rapid change 7.11 Extinction Can be natural or human caused If something goes extinct it can open up opprotunities for other species 7.12 Variation Genetic diversity Diversity of the ecosystem = inc biodiversity Less likey to be 7.13 Origins of Life on Earth No oxygen on earth 4.6 billion No ozone layer Tons of UV radiation High ocean levels Vooacanic eruptions RNA was the first genetic material DNA is dependant of RNA in