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| feed on living things and produce organic materials |
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| an existing gene can be modified by mutations in its DNA sequence |
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| an existing gene can be duplicated so as to create a pair of closely related genes within a single cell |
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| 2+ existing genes can be broken and rejoined making a hybrid gene |
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| a piece of DNA can be transferred from the genome of one cell to that of another |
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| genes in 2 different species that derive from the same ancestral gene in the last common ancestor |
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| (Pseudocell) not cells, have DNA/RNA but can't replicate out of the host cell. Have protein coat, no plasma membrane |
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| (Pseudocell) infectious RNA particle can reproduce, cause disease, but doesn't conserve energy |
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| (Pseudocell) Infectious protein particle, no DNA, no membrane, no cell wall. Can only get ingested through cell wall |
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| makes parts of the ribosome |
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| double layer membrane, separates DNA from cytoplasm, continuous with the ER |
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| double layer membrane, separates DNA from cytoplasm, continuous with the ER |
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| plugged with nuclear pore complex |
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| unused genes (dark color) |
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| actively used genes (light color) |
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| Double membrane bound nuclear envelope containing DNA. Nuclear pores that act as gates to regulate movement on RNA, ribosomes, and chromosomes. Nuclear Lamina (scrapholding inside nuclear envelope to define nucleus' shape), Cytoskeleton (basket network of microtublues over nucleus), Chromatin (DNA and its packaging), Nucleolous (makes RNA and ribosomal pre-cursors) |
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| Phospholipid bilayer (fluid mosaic model). Contains Proteins that carry out specific functions. Functions proteins carry out: transport, structure, recognition. Eukaryotes and Prokaryotes have plasma membrane. |
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| Provides mechanical structure (functions like cell wall). Strength is based on fibers (mechanical properties). Rigid structure outside plasma membrane. |
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| Membrane bound structure with a standardized structure |
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| Energy conservation center. Double membrane bound. More mitochondria when more metabotically active. Carries out cellular respiration to make ATP. Outer membrane is porous and continuous. Contains own circular DNA to make proteins for own use. Highly folded inner membrane to increase surface are to pass proteins. Contains own genome. Can fuse together to make less or can be ingested. |
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| Don't produce a lot of ATP. In plant and algal cells. Has own genome. Bigger than mitochondria. |
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| Chloroplast (double membrane) thylakoid (light synthesis), grana. Major pigment is chlorophyll. Has own circular DNA. Stoma (dark reactions). |
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| Protein synthesis. Studded with ribosomes. Proteins end up in exocytosis or in other organelles in cytoplasm. |
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| Lipid synthesis (vast majority made here). Continuous with rough ER. Lipids end up in cytoplasm. |
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| Has few ribosomes. Protein trafficking. |
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| Ribosomes float around, available to make proteins depending on where they are needed. |
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| A series of 4-5 disc-like sacs held by cellular skeleton. Glycosylation- stick on a carbohydrate |
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| Single membrane organelle |
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| Small vacuoles, rely on lysosomes instead. Can be multiple vacuoles. |
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| Defined strucutre (95%). Central vacuole swells with water from turgor pressure. Drives growth of individual cell (enlargement) allowing cells to expand in a direction where cell is at its weakest. Cellulose cell walls allow parts to be pushed out. Turgor pressure allows cells to keep rigidity. |
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| Spherical, breaks down H2O2 into H2O and H2 because H2O2 is very toxic to cell, causing DNA damage. Detoxifies organelles. Uses enzymes called Catalase and others. Widely distributed in cells. |
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| Unique to plants. Involved in metabolism. Breaks down fats into units that make ATP |
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| Cellulose based cell wall. Glyoxysomes. Plastids. Large central vacuole. |
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| (Fiber in cytoskeleton) Long hollow filaments, aprox 24nm in diameter with varying length. Made of helical tubulin. Pulls chromatin apart during cell division. |
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| (Fibers in cytoskeleton) Long, solid, rod0like structure (filaments) about 68nm in diameter. Moves things around. Made of actin. Takes part in muscle contraction. |
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| (Fibers in cytoskeleton) Highly regulated with diameter b/w 6-24nm comprised of vimentin and laminin. Function depends on protein. Makes up nuclear lamina. Structure-Holds golgi apparatus together, holds all structure together. |
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| Cell wall. Gram negative (red) vs. Gram positive (purple). Different protein filaments- Ftsz: tubulin (acts like microtublues), MreB: acting (acts like microfilaments). |
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| Makes it stain purple that is a gram positive cell wall. In gram negative, pepticloglycan is small and protected by outer membrane |
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| In gram (-) is what makes you sick. It is an endotoxin. |
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| Cellular Junction I(intracellular communication). Only in plants. Extends between 2 adjacent cells. Extends a channel across cell wall into adjacent cell. |
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| ER that extends from one cell to another and acts as a plug and messenger line |
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| Cellular Junction I (intracellular communication). In animal cells. Uses connexons (open channel) that form pores between 2 adjacent cells. Makes a little pipe. Allows direct communication. |
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| (Structural Junction) Strong plaque backbone. Found in digestive tract. Porous to allow ions and water to float between. Anchored to intermediate cytoskeleton and cells providing a lot of strength to hold two cells together. Cadherins form a strong junction and anchor to microtubules (plaque). |
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| (Structural Junction) Not as strong as desmosome. Simple junction. Doesn't require energy to assemble. Can disassemble. Allows cells to interact using zipper-like structure like Desmosomes. Focal Adherens: stick cell to substrates |
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| (Structural Junction) Water tight. Flexible. Tight junction (not a lot of strucutre)- cells actually share common membrane for a bit, desmosomes are in there for strength. Septate Junction- in invertebrates where plasma membrane comes together, more organization, provides invertebrates ability to form water tight layer. Subarin layer (plant cells)-modify cell wall by secreting subanin (waxy substance), forms water tight barrier. Direct extra cellular matrix connection (direct EMC)- simple temporary junction used for migration of cells, allows cells to interact without more organized structure, basically an extra cellular matrix connection |
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| (Strucutral Junction) A "sticky glue" in plant cell walls that "glues" cell walls together |
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| Structural (microscopy). Biochemistry (Fractionate cells into component parts). Molecular (genetic- examining blue pring of all cells (genes)). |
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| Structural (Microscopy). What affects image quality? |
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| Contrast- what gives an image color, etc. (Stains vs. Optics). Magnifications- how an image can be made bigger (size of the object). Resolution- detail (smallest distance which you can see 2 different points as 2 distinct objects instead of blurred into one object). |
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| Glass lens used to focus light. 0.2 micrometes (0.5 micrometers) resolution. Mitochondria looks like a dot. |
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| Electromagnets focus electron beam. 0.1 nanometers resolution. See individual christae membranes. Mainly can observe dead cells. |
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| (Type of light microscopy) Simple use of stains and dyes are needed for contrast |
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| (Type of light microscopy) Split light beam (a way to see objects without using dye) |
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| Differential Interference Contrast |
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| (Type of light microscopy) Sees 3D shadows with phase contrast that allows us to see live cells (uses polarized light) |
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| (Type of light microscopy) Light with a higher resolution. Fluorescent dyes or immunocytochemistry (easy to use). Add Fluorochrome to cell (a dye) and it binds to specific component of cell making it glow. GEP or Fluorescent Analog Cytochemistry. Confocal Scanning Laser Microscopy. Fluorochrome- Emission (have to excite fluorochome to see emission) |
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| (Type of Fluorescent Microscopy) Take fluorochrom and covalently attach it to specific antibody, which have high degree of specificity. You have protein x and take protein x. Inject protein x in animal so antibody is made and binds to protein x. Draw blood and insolate antibodies Anti-Protein x --(animal name)-- antibody. Primary antibody that recognized protein is achieved. |
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| excited by shorter wavelength of light and emits light at longer wavelength |
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| tags desired protein with fluorescent tag, which is excited by specific wavelength and gives off light at higher wavelength |
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| GFP: Green Fluorescent protein (jellyfish) |
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| (Type of fluorescent microscopy) Clone is made of recombinant protein. Allows you to see live cell. |
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| How Does a Fluorescent Microscope Work? |
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| Light source: mercury arck lamp. Goal is to expose sample to specific excitation wavelength. Light hits barrier filter that only lets blue light b/w 450 and 490nm. That light hits dichrotic mirror that reflects light thats below 510nm. Cuts fluorescent signals passing specific green fluorescent emission b/w 520 and 560nm. |
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| (Type of electron microscopy) Higher resolution (0.1nm). Cross sections: very thin sections of cell. Really dead cells. |
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| Scanning Electron Microscopy |
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| (Type of electron microscopy) 3D "surface" images. Lower resolution. No internal strucutre. Visualize through shadowing. |
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| Fixation (Specimen Preparation for Electron Microscopy) |
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| 1) Preserves structure using Aldehydes (causes total cell death) and Alcohols (make things clump) |
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| Post Fixation (Specimen Preparation for Electron Microscopy) |
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| 2) Fixes tissue and acts as a stain. Osmium Tetroxide: heavy metal that causes membranes to be an intense black color. |
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| Embeded and Section (Specimen Preparation for Electron Microscopy) |
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| 3) Embeds tissues so its held together when cut. Paraffin (LM) or plastic (EM) hold together the cell. Dehydrate, embedded, sectron (microtone) |
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| Stain (Specimen Preparation for Electron Microscopy) |
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| 4) Histological dyes vs. Heavy metals. What you see is a capture of a photograph image directly- electrons hit the photographic film. |
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| Fixation (Specimen Preparation for Electron Microscopy (Scanning)) |
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Definition
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| Post Fixation (Specimen Preparation for Electron Microscopy (Scanning)) |
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Definition
| 2) Not required in light microscopy |
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| Stain (Specimen Preparation for Electron Microscopy (Scanning)) |
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| 3) Heavy metals blown across specimen on angle. Makes replica (metal), you put that into microscope so youre looking at mold of tissue, not actual cell |
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| Light Microscopy (Preparation) |
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| 1) Fixation. 2) Embedded and Section (Parafin)- not done in Electron Microscopy. 3) Stain. |
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| Dissociate Cells of Interest (Biochemistry) |
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Definition
| Mechanical mechanisms need broken (ie. Desmosomes need taking out) |
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| Ways to Isolate Cells of Interest (Biochemistry) |
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| Centrifuge- most common type that isolates based on size and shape. FACS (fluorescent activated cell storing)- Sorts based on fluorescent tag. Cellular Fractination- Ultra centrifugation, chromotography (separates based on physical properties, ion exchange: charge separation, hydrophobic-hydrophobicity, gel filtration-separate by size). |
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| Microsequencing or MaLDI-TOF (proteins from mixture). Electrophosis/Western Blotting- extract everything and reconstruct. X-ray crystallography- have to have rich amount of protein, gives 3D structure of protein. |
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| Ultracentrifigation: 1-Cell Homogeny (test tube of mixed population of cells, low speed). 2-Low Speed (pellet contains nuclei and cytoskeletons (cell debris), theres a vacuum so no heat build up). 3- Supernate (liquid) and spin harder (pellet contains particular organelles (mitochondria, peroxisomes)). 4- Spin again (ultracentrifugation) (microsomal pellet (vesicles, chunks of ER and golgi apparatus)). 5- Spin more (ribosomes, centresomes). |
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| Monitor changes in levels of specific proteins detects specific protein |
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| Electrophyesis (Western Blotting) |
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| separates molecules through some matrix (separated DNA molecules through matrix). Put in Agarose material |
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| Polyacrylamide (Western Blotting) |
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| separates complex mixture of proteins. Sorts by size. Little things migrate further than large things. |
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| Coomassie Blue (Western Blotting) |
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| Stains gel and each band represents some amoutn of a specific protein. |
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| SDS-Page (Western Blotting) |
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| Sodium dodectal sulfate-detergent. Coats proteins with negative charge. Denatures proteins, knocks structure apart. Coats denatured, linear proteins with negative charge. Molecules go through as a function of size. Page: polyacrylamide (matrix, gel electrophylesis). Electrophylesis separates by pH first, then by size. |
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| Transfer (Western Blotting) |
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| Takes gel and you lay a membrane on top that binds to proteins (PVDF). Proteins stick to membrane, still separate by size. Repeat with primary antibody which binds to protein. Attach with secondary antibody which had enzyme attached. |
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| Detection Method (Western Blotting) |
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Definition
| Color change- AP (alkaline phosphocatse (enzyme) you add a substrate, giving you a color). |
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| Isolate Gene (Western Blotting) |
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| 1- Screen cDNA or genomic library. cDNA library: complementary DNA extracting RNA and reverse transcribe to get DNA, just shows copies of expressed genes. Genomic library: raw DNA protein coating region, junk DNA, etc. 2- PCR: More direct, works less frequently. To pull out gene youre interested in using, screen library with DNA probe which is fragment of that gene |
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| Clone Gene (Western Blotting) |
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| Copy and insert into vector in host organism. Vectors: cosmids, plasmids, YAC (yeast artificial chrom), BAC (bacteria artificial chrom). Transformation: putting it into bacteria. Transfection: mammalian. |
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| Analyze (Western Blotting) |
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Definition
| 1) sequence. 2) mutation analysis. 3) In Vivo Studies |
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| Reaction Enzymes (Western Blotting) |
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| Cohesive ends (overhang of single stranded DNA) |
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| Central part of definition of life- distinguishes life from other processes. All cells store their heredity information in a code (DNA). |
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| Cells Replicate Hereditary Information |
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Definition
| Nucleotide: monomer in DNA strand with sugar and base. Adenine binds with thymine, cytosine, and guanine. Bonds b/w base pairs are weak, so DNA can be pulled apart without breaking backbone. Four Amino Acids. |
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| Cells Transcribe Portions of Hereditary Information (RNA) |
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| Production of RNA and proteins. Transcription: segments of DNA sequence used as templates to guide synthesis of shorter molecules of RNA. Translation: RNA molecules direct synthesis of polymers proteins |
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| Cells Use Proteins as Catalysts |
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Definition
| Protein: Unbranched polymers and form most of cells mass. 20 types of amino acids. |
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| Cells Translate RNA into a Protein |
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Definition
| 3 nucleotides at a time (codon) are read out for 1 amino acid in a protein (done by tRNA). tRNA molecules are brought together by mRNA. tRNA's matched up by base pairing anticodons with each of its successive codons. Amino acids are linked. |
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| All Cells Have Free Energy (ATP)/Energy Conversion |
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Definition
| Required for synthetic reactions. The greater the binding energy, the reduction of something being mismatched in DNA transfer. |
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| Cells Function as Biochemical Factories |
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Definition
| Cells keep simple molecules to synthesize DNA, ATP, RNA, etc. |
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| Cells Have Plasma Membrane |
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Definition
| Maintains internal and external environment |
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| Cells Have At Least 400 Genes |
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Definition
| Mycoplasma are good example: small bacteria. A typical cell can get away with 400 proteins. |
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