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BIO 130 MIDTERM
bio 130 midterm memorization
| definition of cell | The fundamental unit of life |
| 3 scientist who formulated cell theory | Schleiden, Virchow and Schwan |
| cell theory | 1. all living organisms are made up of 1 or more cells 2. ever cell is the structural and functional unit of life 3. cells can only arise from pre-existing cells |
| exceptions to cell theory | viruses, viroid's and prions |
| viruses | - need host cell to live - need host cell to replicate - only small nucleic acids covered in protein coat ( no cell structure) |
| viroid's | - small circular RNA ( no protein coat or cell structure) - need host replicate |
| prions | - no nucleic acids - proteinaceous infectious particles |
| Cell properties | 1. Cell membrane 2. Genetic program 3. capable of producing more of themselves 4. Acquire and utilize energy 5. carry our chemical reactions 6. Mechanical activitives 7. respond to stimuli 8. self regulation |
| cytoplasm | ALL contents found inside cell membrane minus the nucleus |
| cytosol | jelly like internal fluid environment of cell ( cytoplasm minus organelles) |
| gene | the DNA code needed to produce a functional product |
| central dogma | flow of genetic information DNA-RNA-Protein |
| Capable to produce more themselves | ability to duplicate genetic material before division |
| Carry out chemical reactions | metabolic pathways, ex; glycolysis |
| Engage mechanical activities | transportation in and out |
| Respond to stimuli | have receptors they can comprehend |
| Capable of self regulation | if not causes this such as cancer |
| Eukaryotes descended from which domain | archaea |
| Prokaryotes | single celled, no nucleus or membrane bound organelles, single circular chromosomes, rely on cell wall for internal structure, reproduce through binary fission |
| Bacteria | many have plasmids, have cell wall surrounding cell membrane |
| Archaea | isoprenoid cell membrane, live in extreme habitats |
| Protists | mainly single celled, colonies ex: Algae, water molds, slime molds, protozoa |
| Fungi | chitin cell wall, heterotrophs, ex; yeast, rusts, smuts , mildews, molds mushrooms |
| heterotrophs | dependant on preformed organic molecules from energy- absorb directly from the environment |
| Plants | multicell, cell wall of polysaccharide's, vacuoles full water, intercellular connections called plasmodesmata, autotrophs |
| autotrophs | produce their own food, convert suns energy into chemical energy |
| animals | multicell, no cell walls, heterotrophs, early development |
| Organelles in EMS | specialized organelles and structures for cellular activities - nuclear envelope - endoplasmic reticulum ( both) - Golgi apparatus - lysosomes - vesicles - plasma mebmbrane |
| organelles NOT in EMS | mitochondria, chloroplasts, peroxisome's, ribosomes, nucleolus cytoskeleton, centrosomes, cilia and flagella |
| Model Organism | non human species used to understand biology |
| lysosome | contains enzymes to break down organic molecules, pH of 5 |
| cytoskeleton | structure on inside of plasma membrane that allows stability ( other organelles attach to it ) |
| peroxisomes | enzymes of hydrogen peroxide used to breakdown toxins |
| nucleus | stores genetic information |
| nuclear envelope | protects the nucleus |
| Golgi apparatus | packaging and processing of lipids, proteins and cards |
| pure element | element that contains only 1 atom |
| orbital can hold a max of | 2 electrons |
| multiple atoms | molecules |
| covalent bonds | valence electrons are shared, can be polar or nonpolar depends on electronegativity( if 1 pulls more equals polar) |
| strongest type bond | covalent |
| Ionic bonds | electrons are given, significant difference in electronegativity, creation of ions when dissolved in water split apart |
| cation | extra protons relative to electrons |
| anion | extra electrons relative to protons |
| Ionic in water | when dissolved in water ions are pulled apart and become surrounded by water molecules, hydrogen will associate with the anion ( due to neg charge) and oxygen will associate with cation ( post change) |
| water chemistry | medium of life( most abundant in bio), can dissolve more molecules than anything else, ( universal solvent) Polar, |
| Hydrogen bond | weak bond formed between an electronegative atom and a hydrogen atom that is already covalently linked to another atom , H atoms form H-bonds with highly electronegative atoms ( N, O , F) |
| pH | the measurement of concentration of proton's in a solution |
| enzyme rules | - highly specific - required specific pH - Lower the activation energy as a catalyst - fit substrate - proteins |
| organic molecules | contain carbon |
| Organic molecules | proteins, nucleic acids, carbs, lipids |
| which organic molecules is not a polymer | lipids |
| condensation reaction | monomers combine with each other to from covalent bonds and water molecules are released as by-product, requires energy |
| hydrolysis | polymers are broken down into monomers and water is inserted across the bond |
| organic molecule with largest variety of functions | proteins |
| proteins functions | - enzymes - transport - cell signalling - movement - support - defense |
| physiological pH | 7.4 |
| zwitterion | a polypeptide that contains an equal number of positive and negative functional groups and net charge is 0 |
| peptide forms | carboxyl releases a oxygen atom and the nitrogen loses two hydrogen atoms to produce water |
| nucleic acids | encode genetic information in the sequence of nucleotides. DNA and RNA are polymers of nucleotides |
| structure nucleotides | nitrogenous base ( 2 types) , 5 carbon sugar, one or more phosphate group |
| 2 types of nitrogenous bases | pyrimidine: base that contains single ring ex: cytosine, thymine and uracil purines: base contain double rings ex: adenine and guanine |
| nucleoside | only a sugar and base no phosphate |
| nucleotides | 3 parts, import cell signals ex: AMP or cAMP, cleave of phosphate in to release energy, act as coenzymes/factors, |
| coenzymes/ factors | organic non protein molecules needed for enzyme functions. ex: adenine-containing nucleotides combine with vit. B, or Nicotinamide ( Vit. B3 adenine dinucleotide) |
| connection of nucleotide's | forms DNA and RNA through phosphodiester bonds |
| directionality of RNA and DNA | formation of the polypeptide bond in between 3 prime on sugar and phosphate. start is called 5 prime and nucleotides are added to the 3 prime end |
| how is DNA and RNA built | 5 prime to 3 prime |
| nucleoside | only a sugar and base no phosphate |
| carbohydrates ratio | 1:2:1 of c h and o |
| nucleotides | 3 parts, import cell signals ex: AMP or cAMP, cleave of phosphate in to release energy, act as coenzymes/factors, |
| coenzymes/ factors | organic non protein molecules needed for enzyme functions. ex: adenine-containing nucleotides combine with vit. B, or Nicotinamide ( Vit. B3 adenine dinucleotide) |
| connection of nucleotide's | forms DNA and RNA through phosphodiester bonds |
| directionality of RNA and DNA | formation of the polypeptide bond in between 3 prime on sugar and phosphate. start is called 5 prime and nucleotides are added to the 3 prime end |
| monosaccharides and functions | Glucose: photosynthesis and CR Galactose: dairy products Fructose: sweetener |
| how is DNA and RNA built | 5 prime to 3 prime |
| oligosaccharides | few sugars linking together |
| carbohydrates ratio | 1:2:1 of c h and o |
| disaccharides | sucrose- table sugar |
| functions carbs | energy source and structural molecules |
| sugars and proteins | glycoproteins |
| simplest carbohydrates | saccharides contain 5-6 carbons and linear or cyclical |
| sugars and lipids | glycolipids |
| what form carbs normal exist | cyclical as more stable, less reactive and easier to break off |
| polysaccharides | lots of sugars together, long term energy ex: starch |
| monosaccharides and functions | Glucose: photosynthesis and CR Galactose: dairy products Fructose: sweetener |
| how become cyclical | carbon in the aldehyde or ketone group forms covalent bond with oxygen of the hydroxyl group |
| oligosaccharides | few sugars linking together |
| disaccharides | sucrose- table sugar |
| sugars and proteins | glycoproteins |
| sugars and lipids | glycolipids |
| polysaccharides | lots of sugars together, long term energy ex: starch |
| molecules that contain carbon | organic molecules |
| membrane functions | compartmentalization selectively permeable transporting scaffold for activities responding to signals intracellular interactions energy transduction |
| glycolipids | crab with a lipid attached |
| glycoprotein | car with protein attached |
| cell membrane components | carbs, lipids and proteins |
| micelles | spheres that form when a phospholipid head is too big and bulky and the 1 hydrophobic tail is buried |
| bilayer | smaller heads and 2 hydrophobic tails |
| liposome | added test tube of water and spontaneously form enclosed bilayers, most effective, self healing and will spontaneously rearrange themselves |
| membrane features | dynamic, continuously moving, forming and reforming |
| affects of fluidity | length tails, double bonds and cholesterol |
| Length tails on fluidity | longer the tail the less fluid |
| double bonds on fluidity | less double bonds is less fluid. mor double bonds more fluid |
| cholesterol on fluidity | inserts into the bilayers. can control fluidity dependant on the temperature " buffer" if cold. cholesterol will be more fluid and if hot cholesterol will be more solid . amphipathic in nature |
| lipid rafts | specialized microdomains that serve as platforms for various cell processes, moves laterally, allows to be dynamic and specific functions |
| integral protein | permanetly associated with the membrane and can span the entire lipid bilayer they are transmembrane |
| peripheral proteins | temporarily associated with membrane via covalent bonds. can be cytoplasmic ( in cell) or extracellular( out cell) |
| membrane proteins functions | transporters receptors enzymes anchors |
| membrane carbs | always face outwards, covalently linked to either a protein or lipid ( glycoprotein and glycolipid. |
| endoplasmic reticulum | synthesis of lipids and protein's, largest organelle, network of interconnected tubes and flattened sacs , lots SA from highly folded nature |
| Golgi apparatus | modifies proteins and lipids produced by the ER, acts as a sorting station |
| lysosomes | enzymes that breakdown all macromolecules |
| mitochondria | specialized organelles that harness energy for the cell |
| cytoskeleton | protein scaffold that provides cell structure |
| plant cell contains all but also | cell wall( support) vacuoles ( turgor's pressure) chloroplasts ( convert energy into sunlight) |
| Do all cells have a cell membrane | FALSE |
| Endomembrane system | eukaryotic cells with internal organelles that are surrounded by membranes that interact together physically or through vesicles |
| why have endomembrane system | allows specific functions to take place within defined spaces of the ell |
| organelles in the EMS | plasma membrane and nuclear envelope ER and Golgi apparatus lysosomes vesicles |
| inner most organelle of EMS | nucleus |
| nucleus | a double membrane, inner and outer. has nuclear spores for molecules to travel in and out, spores give communication with rest cell |
| nucleus to ER | nuclear membrane is physically continuous with the ER |
| lumen | the interior space of the flattened sacs in ER |
| rough ER | ribosomes attached- protein synthesis can also be free floating |
| smooth ER | no ribosomes, produce vesicles to move freely, site of fatty acid and phospholipid synthesis lots of SER are specialized to lipid production |
| golgi apparatus | - further modify proteins and lipids from ER - sort proteins and lipids to move to final spot - add carbs to proteins or lipids |
| cisternae | flattened sacs i Golgi apparatus, surrounded by small vesicles which transport proteins from the ER to the Golgi and Golgi to cell |
| glycosylation | ex of enzymes in Golgi, all performed in different region and very specific. this is process of carbs covalently linked to lipids or proteins or aa |
| lysosomes | specialized vesicle from GA, has proton pump to keep pH 5, recycle unneeded macromolecules |
| membrane organelles not in EMS | mitochondria and chloroplasts |
| smiliarity in mitcon. and chloro. | specialized in harnessing energy and semi autonomous |
| semi autonomous | grow and multiple independently and contain their own circular genomes |
| mitochondria | create ATP, rod shaped, |
| outer membrane mitochondria | integral proteins that are porins |
| inner membrane mitochondria | highly convoluted ( twisted and folded) this has ETC and ATP synthase |
| intermembrane space | aqueous compartment between the 2 membranes |
| matrix | kerbs cycle, ribosomes and DNA |
| chloroplasts | where photosynthesis occurs, suns energy to make simple sugars, double membrane |
| thylakoid | internal membrane bound compartment, light collecting pigments ( chlorophyll) which makes green. flattened sacs |
| lumen | space inside thylakoid |
| grana | orderly stacks of thylakoids |
| stroma | space surrounding thylakoid |
| origin chloroplasts | and endosymbiotic relationship between and cyanobacterial cell that had been engulfed by a eukaryotic cell |
| origin of mitochondria | free living bacteria, originated as endosymbiotic bacteria - proteobacteria |
| theory 1 | eukaryotic cells started from ancestral archaeon and later incorporate the proteobacterial cell |
| theory 2 | eukaryotic cells evolved from symbiosis between archaeon and proteobacteria |
| movement into cell | influx |
| movement out of cell | efflux |
| net flux | when 1 exceeds the other - one more dominant |
| passive transport | no energy required, driven by concentration gradient ; simple and facilitated diffusion - nonpolar molecules, small unchargered polar |
| facilitated diffusion | down conc. gradient, carrier and channel protein |
| carrier protein | specific molecule binds to transporter, triggers conformational change to protein, molecule now exposed to opposite membrane surface and diffuses down concentration gradient |
| channel protein | integral proteins, selectively permeable, some have gated channels |
| osmatic pressure | the tonic of the solution |
| crenation | hypertonic situation in animals where cells shrivel and die |
| plasmolysis | hypertonic situation in plants pull away cell wall and die |
| hemolysis | animal red blood cell burst due to hypotonic state |
| turgid | turgor's pressure in plants due to hypotonic state |
| active transport | movement against concentration gradient, requires energy, protein carrier |
| sodium potassium pump | 3 na out 2 k in |
| ATPase | the transport protein to move na out and k in |
| electrochemical gradient | energy stored in concentration gradient from primary active transport, both electrical and chemical component drives secondary active transport |
| secondary active transport | movement of molecules against their gradient due to the electrochemical gradient from active transport |
| antiport | 2 solutes move in opposite directions |
| symport | 2 solutes move in the same direction |
| exocytosis | vesicle fuse with the cell membrane, to move out, budded from EDMS, meets membrane and re fuses emptying contents to extracellular space |
| endocytosis | material outside cell brought into cell through vesicle that can fuse with other organelles. cell membrane makes the vesicles and pinches off |
| invaginates | forms a pocket around the target material |
| phagocytosis | uptake of particle matter, this is the delivery to a lysosome via phagosome. phagosome and lysosome fuse to make a secondary lysosome - actives lysosomal hydrolic enzymes, contents are digested in secondary lysosome |
| benefits of phagosomes | nutrition defense ( macrophages and neutrophils) and enzymes |
| pinocytosis | cell drinking, extracellular fluid taken without recognition, not merge with lysosome |
| receptor mediated endocytosis | receptor proteins for specific substances, very percise |
| coated pit | site where receptors are concentrated- the indented surface |
| clathrin | attached to the cytoplasmic side, brings vesicle into cell ad delivered to endosomes |
| endosomes | network of tubes and vesicles, early= by peripheral region late= interior part of cell |
| virulent | ability to cause disease |
| DNA is read | 5 prime to 3 prime or 3 prime to 5 prime, typically always 5 to 3 if not specified |
| DNA grows in the | 5 prime to 3 prime end |
| bases are added to the | 3 prime end |
| hydroxyl group ionization | 2 negative charges on the phosphate group at cellular pH |
| difference of 5 prime to 3 prime end | polarity |
| percentage | c=g a=t |
| which direction does DNA coil | to the right to allow other molecules to interact |
| features of DNA | double strand, helix shape, antiparallel, outside contour are grooves |
| A | T |
| C | G |
| purines | Adenine and Guanine |
| pyrmides | Cytosine and Thymine |
| Bond of A and T | two hydrogen bonds |
| Bond of C and G | three hydrogen bonds |
| Stability of DNA | large number of h bonds base stacking ( interaction between bases ontop of eachother) |
| Why h bond beneficial | allows it to be undone easily |
| Genome | the genetic material of an organism |
| Housekeeping genes | genes that are always expressed |
| gene | unit of heredity affecting one or more traits of an organism, a DNA sequence that corresponds to a specific protein |
| Gen expression | production of a functional gene product such as protein |
| Transcription | DNA into RNA |
| Translation | RNA into a protein |
| Central Dogma in EUK location | in nucleus and translation in cytoplasm |
| Central Dogma in PROK location | no nucleus so all occurs in cytoplasm |
| 5 prime end of DNA | monophosphate |
| 5 Prime end of RNA | triphosphate |
| RNA features | - single stranded - Uracil - Triphosphate - polarity - shorter - more complex shapes - less stable - ribose sugar ( hydroxyl on 2 c) |
| DNA features | - x2 starnded - helical - thymine - longer - more stable - deoxyribose - monophosphate |
| Transcription enzyme | RNA polymerase |
| direction of polymerase, which end added to | 3 prime to 5 prime, added to 3 prime end |
| direction RNA grows | 5 prime to 3 prime |
| DNA template strand is read in | 3 prime to 5 prime |
| bacteria initation mediated by | sigma protein, 1 protein |
| General transcription factors | 6 proteins that work together to initiate transcription. bind to promotor region |
| transcriptional activator proteins | bind to enhancer sequence to recruit RNA pol 2 |
| Protein required to start transcription P v E | P: 1 E: 6 |
| initiation of transcription in EUK | the looping of DNA so that the activator proteins come into contact with the general transcription factors proteins |
| RNA bubble is | 14 base pairs long |
| RNA - DNA duplex | in bubble 8 pairs long |
| steps of initiation | - General factors bind to TATA box - Activator proteins bind to enhancer sequence - RNA pol 2 binds to TATA box ( GFS) - DNA loops so that activator proteins come into contact with General transcriptional factors creating the Mediator Complex |
| Process of polymerization reaction | - RNA pol 2 detects incoming nucleotides - orients the OH on 3 carbon - O of 3 carbon attacks the innermost phosphate group on nucleotide, provides energy for reaction breaking of 2 phosphates |
| pyrophosphates | 2 incoming phosphates that are released |
| primary transcript | the RNA strand that comes off of the DNA template, it has the information to direct the ribosome to translate the protein |
| Termination PROK | is the mRNA strand doesn't need to be modified as already in cytoplasm |
| Polycistronic mRNA | mRNA that codes the information for more than one gene |
| Termination in EUK | need to be modified so can move out of nucleus safely, Addition of a 5 prime cap, removal of introns and addition of poly A tail |
| 5 Cap | added to 5 prime end, a unique 5 to 5 bond, needed so the ribosome can recognize mRNA, protection |
| Poly a tail | 250 Adenines added to the 3 prime end, transcription termination sequence, protection |
| mRNA splicing | removal of introns ( not expressed) and keeping exons( are expressed) |
| alternate splicing | a single gene can produce many different but related protein in different cells as different splicing |
| amino acids | can be charged at physiological pH ( amino and carboxy groups) |
| hydrophobic AA | folded to interior of protein, R groups will aggregate together because of Weak van der Waals forces adding to stability |
| hydrophilic AA | R groups interact with each other or with water, via H bonds, found on outer surface of proteins |
| Basic AA | Positively charged |
| Acidic AA | Negatively charged |
| Special AA | glycine, proline, cysteine |
| Glycine | The R group is hydrogen, no asymmetrical, small and non polar , free rotation around alpha carbon to nitrogen bond, increases polypetides flexibility |
| proline | R group links back to amino group restriction over C-N bond limits amount of protein folding |
| Cysteine | R group contains SH - allows two cysteines to have a disulfide bridge ( very strong covalent bond) - this bridge can connect different parts of the same protein or different proteins together |
| C terminus | free carboxy end of peptide |
| N terminus | free Animo acid end of peptide |
| synonymously | polymer of AA connected by amino acids is a peptide with protein |
| protein conformation | three dimensional structure of a protein |
| Primary structure | linear sequence of AA, determine shape of the next 3 structures |
| Secondary structure | Alpha helix and Beta sheet, results of H bonding between neighboring AA, between FUNCTNYL GROUPS NOT R GROUPS fixed configuration of the polypeptide backbone |
| Alpha Helix | very stable, right handed to allow other molecules to interact with each other, form due to H bonds on the 4th AA amino group above or below a AA carboxyl group |
| Beta Sheet | pleated folding, H bonds , side by side ca be parallel or anti parallel |
| Tertiary structure | conformation of entire protein |
| Tertiary folding depends on | - spatial distribution of hydrophobic and hydrophilic R groups - Chemical bonds ( H bonds, ionic bonds, disulfide bonds) |
| Tertiary structure determines | areas of protein that will form active sites for enzymes exterior R groups that will affect how protein interacts with others |
| Quantary Structure | many proteins of multiple subunits |
| Homodimer | two identical subunits |
| heterodimer | two independent subunits |
| heterotrimer | 4 subunits split in 2- 2 identical |
| Ribosomes structure | RNA and protein, large and small subunit |
| Euk ribosomes larger than Prok | TRUE |
| A site | Aminoacyl RNA |
| E site | Exit |
| P site | peptidyl site |
| Ribosome moves down RNA | 5 to 3 |
| Codon | nucleotide combination the specifies the placement of an AA |
| tRNA | contain 70-0 nucleotides, bonds with itself to form base pairs, cloverleaf structure |
| Where AA attach to tRNA | 3 prime hydroxyl site |
| anticodon | 3 bases in the anticodon loop |
| How attach AA to tRNA | specific AA are connected by specific enzymes called aminoacyl tRNA synthetases |
| tRNA without AA | uncharged |
| tRNA with AA | charged |
| tRNA to mRNA connection | the anticodon of tRNA will pair with the start codon of mRNA first because they are antiparallel |
| 64 codons | 20 AA, very redundant or degenerate |
| bases on mRNA are read | 5 to 3 |
| Translation Initiation | in EUK : initation complex starts at 5 prime cap. than initiation factors get the small ribosomal subunit and the tRNA for methionine and scan for the AUG codon, once reached large ribosomal unit attaches and initiation factors are released |
| Translation elongation | - tRNA and Met enter A site - Ribosome shift to the right 1 codon - Met in P site while ne tRNA in A site - due to orientation the Met reacts with new AA and forms a peptide bond - ribosome shift kicking old tRNA out and bringing charged tRNA in |
| which direction does the ribosome shift in translation | right |
| Translation Termination | - stop codon is reached - protein release factor binds to A site at stop codon breaks bond to polypeptide - creates C terminus |
| Shine Dalgarno Sequence | In prokaryotes, no 5 prime cap so this is the initiation complex, on all mRNA which allows mRNA to code form numerous polypeptides |
| Affects to Protein Synthesis | - DNA accessibility - RNA processing - Transcription factors - post translational modifications ( phosphorylation) |
| Protein sorting | No signal: stay in cytosol Amino terminal Signal: Chloroplast or Mitochondria Internal signalling: nucleus |
| How proteins sent to ER | - Signal sequence on growing polypeptide which causes to be halted by SRP - SRP binds to ER membrane - SRP detaches, process begins again pushing new protein into channel in ER - protein Get packaged into a lumen to be brought out of cell |
| How proteins anchored to ER | - embedded in ER as it is synthesised - ER channel releases into the membrane ( lumen) - once completed protein stays in the membrane |
Created by:
Mr. Box