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4 atoms of life
carbon, hydrogen, nitrogen, oxygen
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3 uses for radioactive isotopes
1. Treatment of thyroid cancer (radioactive iodide)
2. Auto-radiography--self radioactive picture
3. radio-dating. C14's half-life is 5000 years.
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Octet rule
atoms like to fill their valance shells (except noble/inert gasses)
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Ionic bond
one atom gives another an electron, then the ions are attracted to their charges
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electronegativity
how bad atoms want to fill their valance. O and N want it more that C and H
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Covalent polar
sharing electrons unevenly. H2O--dipole
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nonpolar covalent
sharing electrons evenly. CH4
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hydration shell
when polar water surrounds an ion, like Cl- (anion) or Na+(cation)
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Law of Solubility
Like dissolves like
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Hydrogen bonds
dipole-dipole attraction of separate molecules.
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Properties of Water that make it support life (8)
- 1. hydrogen bonds make high surface tension
- 2. water adheres and coheres
- 3. high heat of vaporization (liquid -> gas)
- 4. high specific heat
- 5. cools by evaporation
- 6. solvent: small and polar so can break up and surround
- 7. Most dense while still in liquid form (4 degrees C)
- 8. can ionize (a small part)
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pH formula
- - log (H+)
- - log (10-5) = pH 5
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pH6 - pH4
100x more acidic (10 x 10)
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Valance
# of electrons needed to fulfill the octet rule
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4 ways that carbon skeletons can vary (creating isomers)
- 1. Length (# carbons)
- 2. Branching (butane, 2-methylpropane=isobutane)
- 3. double bond position (1-butene, 2-butene)
- 4. presence of rings (Benzene, cyclohexane=aromatic)
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isomer
different chemical with same molecular formula
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3 types of isomers
structural, cis-trans, enantiomers
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cis
large groups on same side of double bond (top or bottom)
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trans
large groups on opposite sides of double bond (top and bottom)
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enantiomers
mirror images. Can only exist with 4 different functional groups. Have L (left) and D (right) isomers with different properties (medical). Discovered by Louis Pasteur
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alcohols
-OH, hydroxyl group.
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sugars
1 carbonyl group and multiple OH groups. Either an aldose or a ketose
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Carbonyl
=C=O Ketones (=C=O) inside or Aldehydes (-CHO) at end.
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Aldehyde
-CHO, terminating carbonyl group
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ketone
=C=O Carbonyl group inside molecule
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Carboxyl
organic acid. -COOH (Amine + Carboxyl + R group = amino acid)
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Amino
-N-H2 Amine (Amine + Carboxyl + R group = amino acid)
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Sulfhydryl
-SH, -HS, Thiol
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Thiol
-SH, -HS, Sulfhydryl
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Methyl
-CH3 Methylated Compound
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types of macromolecules
carbohydrates, lipids, proteins, nucleic acids
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Starch
polysaccharide. Plant storage. Made of alpha glucose
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cellulose
type of starch. Made of beta glucose. Plant polysaccharide. Undigestible by animals. Plant cell wall.
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Lipid
defined by being insoluble in water (nonpolar). Not polymers
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fatty acid
long carbon skeleton with carboxyl group at one end. Nonpolar. Part of many molecules (tails).
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Triacyl glycerol
trigliceride, lipid. 3 fatty acid tails attached to 1 glycerol
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trans fats
man made fats with trans double bonds (hydrogenating)
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phospholipids
lipid. Membrane component. Immediatly forms phospholipid by-layer in water. Contains PO4 group (polar, hydrophilic), glycerol and 2 fatty acid tails (nonpolar, hydrophobic). If tail has 1 or more double bonds, it is unsaturated. Otherwise it is saturated.
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dehydration synthesis
removing a water molecule to connect two monomers into a polymer
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Hydrolysis
inserting a water molecule to break apart a polymer
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simple sugars
Carbohydrates [CH2O]n
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Trioses
simple sugar, carbohydrate. C3H6O3
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Pentoses
Simple sugar, carbohydrate. C5H10O5.
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hexoses
Glucose. Simple sugar. Carbohydrate. C6H12O6
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Chitin
polysaccharide of insects and fungi. Dissolving sutures
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glucose
Monosaccharide. Hexose. Carbohydrate. C6H12O6. Aldose. Forms ring.
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Amylose
simplest form of starch (unbranched). Long unbound chain of glucose structures
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amylopectin
starch in a Y shape (like amylose or glycogen)
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Glycogen
animal polysaccharide with lots of ends so it can break down faster.
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Saturated fats
animal fats containing no double bonds, so they freeze easily and are solid at room temperature
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unsaturated fats
plant fats containing at least one double bond. Freezing point is high and they are liquid at room temperature
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cholesterol
nonpolar lipid steroid with 4 fused rings. All other steroids (sex hormones) synthesized from it.
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types of proteins (8)
- enzymatic
- storage (milk (casein), egg whites (albumin), seeds)
- hormonal (insulin, vasopressin, oxytocin)
- contractile and motor proteins (actin, myosin)
- defensive (antibodies)
- transport (hemoglobin)
- receptor (chemoreceptors--smell)
- structural (keratin--hair, nails etc.)
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What are amino acids held together by?
peptide bonds (polypeptide is protein). Polypeptide is a polymer of amino acids
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Amino Acid
amino plus carboxyl group, around an asymmetric alpha carbon. The carbon is attached to these two groups, a hydrogen and the R group.
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Primary structure of Amino Acids
sequence of amino acids
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secondary structure of amino acids
hydrogen bonding in amino acids (alpha helix and beta pleated sheets)
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tertiary structure in amino acids
R-group interactions (hydrogen bonds, hydrophobic interactions, ionic bonds, disulfide bridges)
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quaternary structure of amino acids
multiple polypeptides held together by hydrogen bonds
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Denaturing
changing the function and physical properties of proteins. Cooking egg whites or unwinding overlap (hair).
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Nucleotide
- Monomer of nucleic acid polymer (polynucleotide)
- 1. sugar pentose (DNA and RNA use ribose and deoxyribose. Deoxy has 1 less O)
- 2. phosphate group
- 3. Nitrogenous base
- Have a 5 end and a 3 end, and run antiparallel(highway)
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Nitrogenous bases
- pyramidine (one fused cyclohexane)
- purine (two fused cyclohexanes)
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DNA structure
Polynucleotide. Sugar and Phosphate form backbone, Nitroginous base forms ladder rungs. Hydrogen bonds create double helix.
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Robert Hooke
saw first "prison cells" in cork
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van Leuwenhoek
saw first microorganisms in pond water and semen
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Schleiden and Schwann
cell theory: all life is composed of cells. Cells are the basic unit of life. All cells come from pre-existing cells..
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Resolution
ability to distinguish 2 dots as 2 dots
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Light microscope (LM)
regular microscope, where light passes through the subject.
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electron microscope
shoots electrons through object. Must be placed in a vacuum. Object must be dead. Can see organelles
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Organelles
internal cellular structures
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vital dyes
dyes that allow cells to keep living
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microtome
deli-slicer for cells
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Scanning Electron Microscope (SEM)
coat objects with gold and then excite electrons to get a 3D image on a screen. GOod for topography
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transmission electron microscope (TEM)
see internal structures by coating with heavy metals like lead. Good for internal structures
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phase-contrast
density is amplified to enhance contrast
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differential-interference contrast
exaggerate density to make object look 3D
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fluorescence
inject with fluorescence. Emits visible light
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confocal
takes light from specific planes--sharper images
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Fractionation and Centrifugation
put cells in the blender, then centrifuge them. Weight makes them settle out separately.
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prokaryotes
Bacterial cells. Nucleoid--no membrane to contain DNA. Have ribosomes, plasma membrane, cell wall (proteoglycan), Capsule (polysaccharide slime), Flagella, Fibriae (pilis--sexual reproduction and anchorage).
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plasma membrane
half phospholipids, half proteins (transport proteins), carbohydrate side chain (markers to identify cells--blood type).
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Nucleus
largest organelle in animal cells. Has all DNA. Has double membrane and nuclear pores.
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Nucleolus
ribosomes are made. DNA is contained here. So is chromatin (DNA and protein)
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Free ribosomes
out in cytoplasm. Make proteins that work in cytosol
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Bound ribosomes
create proteins that are secreted from cell, work in membrane or lysosomes
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endomembrane system
nucleus, ER, golgi apparatus, plasma membrane, lysosomes, vacuoles/vesicles. Synthesizes proteins, transport of proteins into membranes or organelles or out of cell, metabolism and movement of lipids and detox of poisons
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rough endoplasmic reticulum
studded with ribosomes, makes membrane proteins. Stores them in lumen of ER (cisternae). Membrane is continous with nuclear envelope. Makes insulin, glycoproteins (proteins with carbs), membrane factory. Grows in place (adds to own membrane)
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smooth endoplasmic reticulum
detoxification (drugs and poisons), stores calcium, synthesizes lipids (oils, phospholipids, steroids)
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Golgi apparatus
"post office". Takes transport vesicles from rough Er in on Cis side, reads them, labels them and sends them out the trans side to the membrane. Cisternae with enzymes. Modifies glycoproteins, membrane phospholipids and makes polysaccharides
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lysosome
"splitting bodies". Little stomachs full of digestive enzymes performing phagocytosis and autophagy. Some are made by rough Er and golgi
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peroxisome
"test tubes". Delicate enzymes are put in peroxisomes to work more efficiently
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Mitochondria
2nd largest organelle. Double membrane (inner folded membrane called cristae), own DNA and ribosomes. Cellular respiration. Glucose+oxygen=carbon dioxide, water and ATP.
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endosymbiosis
when a tiny organism lives within a larger one long enough that they become a part of each other--mitochondria and chloroplasts
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cytoskeleton
microfilaments, microtubules, intermediate filaments. Support, movement, anchorage of organelles, vesicle tracts
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microtubules
hollow tube. alpha and beta proteins. Major components of cilia and flagella. Also serves as spindle apparatus in mitosis. Centrisome hub. Tracks in cell (golgi to plasma), growth of plant cell wall.
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microfilaments
actin filaments. Braided rope. Muscle contraction, cytoplasmic streaming (organisms moving on actin tracks), clevage of cell. Ameboid movement. Bear tension, cell shape (cortex), so it's a gel not a liquid. Microvilli. Cytoplasmic streaming.
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Intermediate filaments
Tough proteins that give cell structure. different from cell to cell. Bear tension. More permanent than others. Hold cell shape, hold nucleus in place. Lamina.
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centrisomes
consists of 2 centrioles. made of tubulin. spindle apparatus in mitosis
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flagella
mostly sperm cells in animal, but in many plants (algae and fungi). involved in locomotion. Also cilia. movement. 9+2 arrangement.
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dynein protein
motor. Bends flagella/cilia and makes it "walk" on microtubules.
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Microvilli
inside of intestine. Convoluted surface of some cells. Plasma membrane's finger-like projections. Underneath each one is microfilament.
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Plant Cell vs Animal Cell
- Plant: chloroplasts, central vacuole, cell wall and plasmodema
- Animal: lysosomes, centrisomes
- Both: Nucleus, smooth Er, Rough Er, Ribosomes, Cytoskeleton, plasma membrane, mitochondria, golgi, peroxisome, flagella
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lamella
proteins that glue the cell walls together.
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Extracellular matrix
outside cell wall, loose mesh of proteins. Communication between inside and outside. In animal, collagen, proteoglycan.
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Desmosomes (animal)
the velcro that bonds cells and tissues.
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gap-junction (animal)
little tubes connecting cells, letting ions and tiny molecules through.
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tight junctions (animal)
the rubberband that prevents things from squeezing between the cells. Found in GI tract.
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chloroplasts
site of photosynthesis (opposite of cellular respiration). Double membranes. Inner membrane is green. Where chlorophyl (pigment) occurs. Thylakoid stacks (green), stroma (fluid) is outside. Has DNA and ribosomes. Mobile--move on cytoskeleton. Plastid.
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central vacuole
big sac of water with ions and chemicals inside. Filler for plant cell.
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Photosynthesis formula
6CO2 + 6H2O--> C6H12O6 + 6O2
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Cellular respiration formula
C6H12O6 + 6O2--> 6CO2 + 6H2O + 36ATP
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Cell wall
plants have 2--elastic primary while growing, secondary more substancial. Made of cellulose. Fights gravity, stops osmosis. Outside of plasma membrane. Microfibrils.
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Plasmodema (plant cell)
like gap junctions in animal cells. Passages that can open, close and dilate to allow proteins and mRNA to enter. Allow lots of communication, so plants act like 1 big super-cell.
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qualitative data
recorded observations that are descriptions, not numbers
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quantitative data
recorded observations of numbers and measurements
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three steps of the scientific method
- observation
- hypothesis
- experimentation
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inductive reasoning
logic in which generalizations are based on observations
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deductive reasoning
logic in which specific results are predicted from a general premise (if-then)
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3 elements of a good experiment
- control group
- repetition
- large, representative samples of all sides
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asymmetrical carbon
C attached to 4 different atoms/molecules
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glycosidic linkages
covalent bonds between monosaccharides by dehydration synthesis, turning them into disaccharides
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