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Principles of Bio 1
Fist Midterm
| Question | Answer |
|---|---|
| Biology Defined | scientific study of living organisms |
| "materialism" | reality is based off of matter, energy, and information (the known physical forces) |
| "vitalism" | opposite of materialism. forces of energy based on unobserved information |
| where do mass, energy, and information come from? | mass and energy come from enviornment. and information is inherited from your parents |
| what defines "life"? | life arises via reproduction and evolution of previously existing life |
| metabolic aspect of life | life is a process with continuous input and output of matter and energy (atoms are not permanent residents) |
| hierarchy of biological organization | ecosystem -> organism -> organs -> tissues -> cells -> organelles -> molecules -> atoms . . . |
| essential elements of life | 25 out of 92 total elements are required major elements - H,C,O,N (96% of total by mass) |
| importance of shape of molecules | responsible for recognition and response in biology (enzyme specificity, membrane transport, signal recognition) |
| polymer | formed by covalently linking monomers ex.) starch, proteins(polypeptides), and DNA RNA |
| benefits of polymers | you can make many different polymers with a small number of monomers -> allows for coping with changing needs |
| hydrolysis reaction | breaks bonds between monomers of a polymer through the use of water (spontaneous reaction) |
| dehydration reaction | removes water molecule forming a covalent bond between to monomers (non-spontaneous) DOES NOT OCCUR IN CELLS!!! |
| synthesis of polymers | activated monomer loses OH molecule and covalently bonds to polymer transfer from activated monomer is spontaneous and does occur in cells |
| proteins | polymers of amino acids - catalytic, structural, transport, and receptor proteins (different structure, different functions) |
| components of an amino acid | amino group (H-N-H) R group (side chain) Carboxyl group (O-C-OH) |
| primary structure of a protein | linear sequence of amino acids |
| secondary structure of a protein | 2 structures 1.) beta pleated sheet structure 2.) alpha helix |
| tertiary structure of a protein | side chains interact to form complex folds to compact structure |
| quarternary structure of a protein | includes all tertiary secondary and primary structures |
| denaturation | protein is unraveled in a sense |
| renaturation | protein reverts back to its normal structure (not always possible) |
| catalytic cycle of an enzyme | substrates fit into specific active site in enzyme and are changed into the products |
| enzyme inhibition | competitive inhibitor binds to active site not allowing substrate to be catalyzed |
| allosteric inhibitor | non-competitive inhibition, inhibitor binds to opposite side of enzyme |
| prokaryotes | no nucleus or membrane enclosed organelles ex.) bacteria, archaea |
| eukaryotes | has nucleus and membrane enclosed organelles ex.) multicellular organisms |
| cytoplasm | cytosol, organelles, and cytoskeleton |
| cell fractionation | separating the parts of a cell to study individually |
| pellet and supernatant | pellet is at the bottom of the test tube during cell fractionation and the supernatant is the rest |
| nucleus | double membrane with nuclear pores and nuclear lamina chromatin DNA ->RNA nucleolus rRNA |
| ribosomes | 2 subunits (large and small) assembled in nucleolus - membrane bound and free - made of proteins and RNA - site of protein synthesis |
| chromatin | made of DNA and protein -DNA -> RNA in nucleolus |
| endoplasmic reticulum | rough and smooth - membrane network of tubes, flattened sacs inside the cytoplasm |
| rough ER | -protein synthesis (membrane, secretory, and other) -carbohydrate attachment to form glycoproteins -phospholipid synthesis (membranes) |
| smooth ER | -tubes connected without ribosomes -synthesis of lipids -detoxification (drugs and alcohol) |
| nuclear lamina | in nucleus -exoskeletal fibers under membrane |
| golgi apparatus | -carbohydrates on glycoproteins get modified -secretory polysaccarides -cells "postal service" |
| lysosomes | bags of digestive enzymes -active at low pH's (~5) -autophagy (self eating) cells "sewage treatment plant" |
| phagocytosis | lysosome digesting food (protist) |
| autophagy | breaking down damaged organelle |
| cytoskeleton | -microtubules -microfilaments -intermediate filaments Functions : maintain cell shape, allows changes in cell shape, supports movement w/in cell, anchors organelles, cell motility site (amoeba, cilia, flagela) |
| cell membrane | basic structure is similar, dynamic Functions : barrier (selectively permeable), sensor, and adhesion (to form tissues) |
| phospholipids | amphipathic -> both hydrophilic and hydrophobic -major molecule of membranes -formed from triglycerides (glycerol + fatty acids) -self assembled -> bilayer (b/c of hydrophilic and hydrophobic ends) |
| integral proteins | proteins inside of the membrane (through the middle of the membrane) |
| peripheral proteins | proteins outside of the membrane |
| G-Protein coupled receptor (GPCR) | -receives signal from molecule outside -G-Protein inside binds to receptor and changes GDP to GTP |
| membrane fluidity | depends on lipid composition and temperature - tails with kinks are fluid - saturated tails w/out kinks are viscous |
| carbohydrates in membranes | found on the outsides of cell membrane -glycoproteins -glycolipids -oligosaccharides |
| functions of membrane proteins | -transport -enzymatic activity -signal transduction -intercellular joining -cell-cell recognition -attachment to the cytoskeleton and extracellular matrix |
| tight junctions | -seal, separate adjacent cells -prevent fluid and solutes from moving across a layer of cells |
| desmosomes | anchor cells to one another |
| gap junctions | intercellular communications |
| membrane permeability | fat soluable and non-polar molecules permeate ex.) hydrocarbons, CO2 and O2 Polar and ionic molecules need special path by means of channels and transporters |
| passive movement | high to low concentration (diffusion free or mediated) |
| active movement | low to high concentration |
| facilitated diffusion | -Channels -Molecules move passively –high to low concentration -Channels and Carriers show substrate specificity -Carriers (Transporters) -passive transport |
| cystic fibrosis | chloride channel defect |
| channels | Specific pathways - Allow diffusion - Some are open in default position - Some are closed in default position - Can be closed or opened by specific conditions |
| active transport | low -> high concentration - requires input of energy |
| membrane potential | electrical force -inside is typically more negative than the outside |
| electrogenic pumps | - Proton (H+) pump - generates Proton Gradient - each proton carries 1 positive charge - generates Membrane Electrical Potential (Voltage) |
| sodium potassium pump | -requires ATP -phosphate becomes covalently bonded to protein - 3 Na+ out and 2 K+ in results in overall negative 1 charge |
| electrochemical gradient | - Membrane potential (electrical force) - Concentration difference (chemical force) - Energy gradient (osmotic force) |
| essential properties of genes | - Contain information - Can be replicated precisely (almost) - Can produce observable traits |
| evidence supporting DNA as genetic material | viruses grow in bacteria -DNA entered cell and proteins didn't so DNA was source of making genes |
| chemical components of DNA | - Deoxyribose - Nitrogenous bases - Phosphate |
| deoxyribose | 5 carbon sugar |
| pyrimidines | Cytosine and Thymine - single ring |
| Purines | Adenine and Guanine - double ring |
| hydrogen bonds in base pairing | A-T --> 2 hydrogen bonds C-G --> 3 hydrogen bonds |
| semiconservative model | each "daughter" DNA has 1 parent strand and 1 new strand |
| conservative model | after replication there is 1 parent molecule and 1 entirely new DNA molecule |
| dispersive model | 2 new strands are both a mixture of parent and new strands |
| Meselson-Stahl Experiment | solidified that the semiconservative model is the correct model for replication |
| origin of replication | starts in bubbles along strand until whole strand is separated ===<>====<>===<>=== |
| synthesis of new DNA | - One nucleotide added at a time - Precursor = deoxynucleosidetriphosphate, which provides energy as well as mass - only goes from 5' to 3' direction |
| topoisomerase | relieves the unwinding strain |
| Helicase | unwinds double strand DNA |
| single strand binding proteins | prevent strand re-association during replication |
| Primase | generates free 3' end |
| leading strand | continuous 5' to 3' - starts with a primer - DNA polymerase III makes a 5' to 3' strand - continues until template is complete |
| lagging strand | synthesizes 5' to 3' in fragments - primase and then RNA primer - DNA polymerase I removes primer and DNA ligase seals the gap |
| okazaki fragment | the fragment produced by the lagging strand in replication |
| telomerase | solves problem of shrinking DNA due to primers at the end of a lagging strand |
| transcription | DNA ----> RNA - certain codons signal for start and end of transcription -RNA polymerase works like DNA polymerase but does not need primer |
| one gene on enzyme hypothesis | enzymes and genes have a one to one relationship |
| flow of genetic information | DNA --> RNA by transcription RNA --> polypeptide by translation one gene - one peptide |
| RNA (ribonucleic acid) | Polyribonucleotide • Ribose instead of deoxyribosesugar • Phosphate • Nitrogenous bases –C, U, A, G. - U instead of T |
| codon | base pairs of 3 to bridge the language gap during translation - can be redundant (uuu and uuc) both go Phe |
| RNA polymerase | quaternary structure - opens up DNA helix -initiates synthesis with NTP -DNA closes behing - termination |
| promoter | - Promoter = Controlling point for gene expression - Every gene has promoter, usually different. - Start point |
| transcription factors (TF's) | - Proteins that bind to promoter - Different promoters require different TFs - Availability of TFsdetermines gene expression |
| elongation | RNA strand joins in a bubble of an unwinding DNA strand |
| transcription termination | RNA transcript and polymerase fall off and DNA returns to helix structure RNA is a single strand molecule complimentary to the DNA molecule -caps are added to strand for ribosome attatchment |
| introns and exons | introns are spliced out of the RNA strand and the exons are joined together |
| pre-mRNA | RNA strand before the introns are spliced out |
| mRNA | RNA strand with caps on end and introns spliced out |
| RNA splicing mechanism | protein snRNA + other proteins --> spliceosome - intron is cut out |
| components of translation | - mRNA - tRNA - amino acid - Aminoacyl-tRNA synthetases - ribosomes |
| tRNA | - decoder -anticodon corresponds to a specific amino acid -anticodon complimentary to codon |
| Aminoacyl-tRNAsynthetase (AARS) | enzyme that catalyzes bond formation between tRNA and amino acid - assures accuracy - 20 different synthetases for different amino acids and tRNAs |
| wobble | relaxed base pairing - some tRNAs recognize multiple codons |
| ribosomes | two subunits - RNA + proteins - provide physical site for translation -have multiple functions |
| translation processes | 1.) Initiation 2.) Elongation 3.) Termination |
| Initiation of translation | -small sub unit of ribosome -mRNA -initiator tRNA |
| Elongation of translation | -transfer of a peptide back to "A" adds one amino acid to the chain -goes back to "P" with translocation - goes back and forth until chain is complete |
| termination of translation | release factor recognizes stop codon (UAG,UUA, OR UGA) -polypeptide is released with GTP |
| polyribosomes (polysomes) | - multiple ribosomes can be on a single strand of mRNA |
| mutation | - Changes in the genetic material - Chromosome changes 50% of spontaneous abortions - Down syndrome (extra chromosome 21) - Smaller changes in DNA Uncorrected errors in replication Caused by mutagens |
| mutagen | agent that causes mutations ex.) Radiation and chemicals |
| effects of mutation (1) | mutations cause change in DNA - altered product --> function altered or absent - biological consequences depend on the function of the product (if it's vital or not) |
| effects of mutation (2) | somatic cells vs. germ cells - somatic cell mutations--> disease ex.) cancer - germ cell --> heritable disease |
| neutral mutation | when the change of one base pair does not effect the amino acid built |
| missense mutation | when the change of one base pair changes the amino acid that was supposed to go - may cause problems |
| nonsense mutation | when the change of one base pair changes the codon to a stop codon - causes premature termination - protein fragment is produced --> no activity |
| frameshift mutation | more common than nonsense - when one extra base pair is added or taken away - shifts the codon pairs down one changing amino acid sequence downstream |
| defense against mutations | proofreading during replication -repair -> 100 enzymes - mismatch repair - excision repair |
| proofreading durning replication | DNA polymerase I and III detect wrong bases and replace them with the right ones |
| mismatch repair during replication | fixes mess up if proofreading overlooks it |
| excision repair | thymine dimer(caused by UV) --> endonuclease --> DNA polymerase --> ligase = repaired |
| metabolism | - The totality of chemical reactions in an organism - can be considered as a web of interconnecting energy transformations |
| biosynthesis | anabolic pathways light energy + CO2 + H20 --> O2 + C6H1206 |
| degradation | catabolic pathways C6H12O6 + O2 --> H2O + CO2 + energy |
| energy | capacity to cause change - kinetic and potential |
| thermodynamics | study of energy transformations |
| 1st law of thermodynamics | conservation of energy - total energy amount remains the same |
| 2nd law of thermodynamics | entropy (disorder) increases - total energy same in quantity but not in quality |
| free energy (G) | ^G= G final - G initial |
| exergonic reaction | net release of free energy ^G < 0 - more energy at the start of reaction "spontaneous reaction" |
| endergonic reaction | needs free energy from surroundings ^G > 0 - more energy at the start of reaction "non-spontaneous" cannot occur by itself |
| closed system | can do work when not at equilibrium but stops when equilibrium is reached |
| open system | can do work continuously as long as input equals the output |
| disequilibrium | maintained in an open system when input is equal to output |
| chemical work | driving endergonicreactions such as the synthesis of polymers from monomers |
| transport work | pumping substances across membranes against the direction of spontaneous movement |
| mechanical work | beating of cilia, contraction of muscle cells, movement of chromosomes |
| energy coupling I | production of glutamine is endergonic and non-spontaneous - but when paired with production of ADP and P the overall process is exergonic and is spontaneous |
| energy coupling II | glutamatic acid + NH3 is endergonic but is spontaneous when paired with ADP and P reaction |
| ATP hydrolysis | ATP turns into ADP and P releasing free usable energy |
| ATP synthesis | ADP +P + energy from catabolism --> ATP |
| glucose | - model food molecule - plants and animals use polymers of glucose for energy storage -Glucose + O2 --> CO2 + H2O + free usable energy |
| glycolysis | glucose --> pyruvate - takes place in the cytosol - energy investment phase (2 ATP) - energy pay-off phase (2 pyruvate, 2 ATP, 2 NADH) |
| NAD+ | another major player in energy transformation - can receive electrons, protons, and energy to become NADH |
| fermentation 1 | yeast cells no oxygen - glucose --> 2 ethanol + 2CO2 + 2ATP |
| fermentation 2 | muscle cells (lactobacter) no oxygen - glucose + 2 ADP + 2P --> 2 Lactate +2 ATP |
| fermentation | continues from glycolysis in absence of oxygen regenerates NAD+ ends with excretion of ethanal or lactate no additional capture of oxidation energy used by red blood cells, micro-organisms etc. |
| mitochondria compartments | two membranes inner membrane in folds called "cristae" matrix inside the inner membrane |
| citric acid cycle summary | Acetyl-CoA (2C) 2 CO2+ 3 NADH + 3 NAD++ FAD ---> + FADH2+ (ATP) + (ADP) + P |
| ATP yield during respiration | glycolysis - 2 ATP citric acid cycle - 2 ATP oxidation - 32-34 ATP |
| chemiosmosis | An energy coupling mechanism that uses the energy stored in a proton-motive force (proton gradient) to generate ATP. |
| ATP synthase | - H+flows from inter- membrane space through synthaseto matrix - Flow rotates rotor, driving conformation changes in catalytic knob subunits - Conformation changes force condensation of ATP + P ---> ATP |
| what is the reason for differences in complexity? | % of gene not coding for protein or RNA - the more complex the organism the greater ----the amount of non coding DNA - number of genes or size of genome do not matter |
| Genome | 1920 by Winkler - gene + chromosome - sum of all information present in a cell |
| open reading frame | from the start codon to the stop codon |
| high throughput techniques used to study genes | 1.) nucleotide sequences of all DNA in the chromosomes of an organism 2.) DNA microarrays- detect all mRNA's transcribed 3.) 2D gel electrophscesis + mass spectroscopy - detect all proteins translated in cell |
| reductionism | study biology by breaking down in to simpler forms assumptions: 1.) know how the simple parts work then you know how the organism works as a whole 2.) what these parts are assembled of --> same characteristics (molecules --> cell) |
| holism | emergent properties - the whole is greater than the sum of its parts ex.) humans have consciousness but single brain cell does not |
| Network Biology (systems biology) | Interactions among the parts are emergent properties - complex systems are a result of networks |
| nodes | the parts of a network system |
| links | the interactions between nodes of a network |
| interactome | interactions between proteins in a cell - lock and key |
| evolutionary properties of life | - growth and development - reproduction -evolution |
| metabolic properties of life | - ordered structure - energy from environment is required - regulation (homeostasis) |
| metabolic aspect of life | all life is an open system - matter and energy in matter and energy out - life is dynamic - turn-over (breakdown and re-synthesis) |
| why we need to know what "alive" means? | - astrobiology (outer-space exploration) - determining death - determining when life starts - maintaining life - self understanding - creating life |
| why is synthesis of life an important biological goal? | - demonstrate our understanding of life - demonstrate the validity of materialism and the lack of a need for vitalistic forces - determine how life got created |
| mycoplasma | - prokaryote (no cell cell wall) - chromosomes are in a circle - smallest free living -pathogens - small genomes (500-1000 Mbasepairs) |
| Venter (biologist) | worked with mycoplasma to synthesize life |
| positive control | chemically synthesized the entire genome - computers tell robots the sequence |
| protein aggregates | - proteins and nucleic acids spontaneously interact (energetically favorable) - also with ribosomes and viruses |
| possible reasons why complete synthesis has not been achieved | - macromolucular parts must assemble in certain order - templates (templates must form to create other molecules) |
Created by:
Lindquist
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