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199 Cards in this Set
- Front
- Back
name the 4 most abundant elements in the human body
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Nitrogen
Carbon oxygen hydrogen |
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List the essential elements other than N,C,O & F.
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Sodium (Na)
Potassium (K) Magnesium (Mg) Calcium (Ca) Phosphorus (P) Sulfur (S) Chlorine (Cl) |
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Atomic weight?
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protons + neutrons
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Term for atoms tendency to establish completely full outer energy levels?
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Octet Rule
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sharing electrons between atoms forms _______ ?
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Covalent bonds
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strongest bond?
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Covalent
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Bond formed by the transferring of electrons?
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Ionic bonds
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Bond due to molecula polarity?
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Hydrogen bonds
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a force due to fluctuating electrical charges?
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Van der Waals Attraction
Includes :dipole-induced dipole, induced dipole-induced dipole. and dipole-dipole |
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term for the repulsion force from water?
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hydrophobic forces
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forces that are weak in water, but in the absence of water are very strong (as in salt).
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Electrostatic attraction
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functional group name for OH
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Hydroxyl
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functional group name for O=C
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Carbonyl
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functional group name for
O=C-OH |
Carboxyl
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functional group name for
H-N-H |
Amino
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functional group name for
O O-P-O O |
phosphate
|
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functional group name for
S-H |
Sulfhydryl
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functional group name for
H H-C-H |
Pyruvate
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How do Ketones differ from aldehydes?
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In ketones the carbonyl (C=O) is placed between two carbons rather than at the end of a carbon skeleton (with a Hydrogen)
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functional group that features a carbonyl group (C=O) bonded in between two other carbon atoms?
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Ketone
eg: acetone is most common |
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Functional group in which a carbonyl group is bonded between the end of a carbon skeleton and a hydrogen.
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Aldehyde
*many fragrances are aldehydes. |
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term for adding a phosphate to a substrate-
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Phosphorylation
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Term for adding a carboxyl group to substrate?
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Carboxylation
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Term for removal of carboxyl?
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De- carboxylation
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Term for removal of a hydrogen from substrate?
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De- hydrogenation
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Term for removal of amino group from substrate?
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De-amination
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4 Major types of macromolecules in cells?
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1. polysaccharides
2. fats/lipids 3. proteins 4. nucleic acids |
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Monosaccharide containing an aldehyde group?
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Aldose
Eg: glucose |
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Monosaccharide containing a ketone group?
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ketose
Eg: fructose |
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similarity and difference between fructose and glucose?
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both are 6 carbon sugars
Different STRUCTURES: Fructose is in the ketose group (contains C=O) Glucose is in the Aldose group (contains H-C=O) |
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Term for isomers in which the geometrical positioning of atoms and functional groups in space differs- MIRROR IMAGES
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Optic isomers
or Stereoisomers |
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Term for isomers in which the atoms and functional groups are joined together in different ways
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Structural isomers
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Configuration when OH group is on the same side as carbon 6?
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Beta Configuration
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Configuration when OH group is on the opposite side of carbon 6?
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Alpha configuration
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define condensation.
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A water molecule is released and two monosaccharides become one polysaccharides.
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define hydrolysis.
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a water molecule is added to a polysaccharide resulting in 2 monosaccharides.
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Term for when a water molecule is added to a polysaccharide resulting in 2 monosaccharides.
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hydrolysis
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what is a sugar derivative?
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When a hydroxyl group of a simple Monosaccharide is replaced by a different group.
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sugar derivative that is the building block of chitin?
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Acetylglucosamine
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sugar derivative with a amine group on carbon #2?
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glucosamine
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sugar derivative with a carboxyl group?
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glucuronic acid
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disaccharide with 2 glucoses?
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Maltose
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Disaccharide with 1 glucose and 1 galactose?
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lactose
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disaccharide with 1 glucose and 1 fructose?
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sucrose
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saccharide with 30-50 sugars?
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oligosaccharide
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saccharide with over 50 sugars?
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Polysaccharide
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polymer of glucose used in energy storage in animals?
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glycogen
(starch in plants) |
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polymer of glucose used in energy storage in plants?
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starch
(glycogen in animals) |
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in the cell walls of plants.
an unbranched polymer of glucose used for structre and other things. |
Cellulose
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glycogen, starch and cellulose are all examples of what kind of sugars?
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POLYSACCHARIDES.
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a large molecule (macromolecule) composed of repeating structural units with covalent bonds
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polymer
|
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This polymer of glucoronic acid and acytlglucoamine is a structural component of cartilage.
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Chondroitin sulfate
(part of proteoglycan) |
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This polysaccharide of glucose enhances WHITE blood cell function.
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Glucan
(the mushrooms!....beta glucan used against tumor cells!) |
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carbohydrates in the human body are stored in the _____.
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liver
|
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a protein "decorated" with oligosaccharide. ?
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glycoprotein
|
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function of glycoprotein?
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-regulates white blood cell extravasation (leakage)
-cell surface proteins for immune response (ID!) -cell-cell interactions structural, etc. |
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polysaccharides "Decorated" with protein?
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Proteoglycans
|
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Function of Proteoglycans?
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mostly structural
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lipids with a carbohydrate attached?
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glycolipids
|
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function of glycolipids?
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component of cell membrane
energy cellular recognition |
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1 meter ^-9?
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nanometer (nm)
|
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1 Liter ^ -6?
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microliter (μL)
|
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which is the preferred light microscope for microbiology which shows the image in 3D?
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interference contrast microscope
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how would you describe the image displayed by a Bright Field Optics microscope?
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grey, low contrast, 2D, light microscope (vs electron microscope)
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which light microscope shows a highly contrasted 2D image?
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Phase Contrast Optics Microscope
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what is the maximum resolution for a light microscope?
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0.2 μm
|
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What is the maximum resolution for an electron microscope?
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0.002 μm
*this is one hundred times more precise than a light microscope! |
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What are the 2 types of electron microscopes and their corresponding resolutions?
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Transmission (TEM): resolution .002 μm in 2D Scanning (SEM): resolution 0.02 - 0.003 μm in 3D |
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What is the central dogma of microbiology?
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Transcription and translation!
|
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What are the macromolecules in microbiology and their corresponding "building blocks"?
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1. Polysaccharides made of sugars. |
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what are the basic shapes of prokaryotic cells?
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spherical, rod shaped and spiral.
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proteins outside the cell which support the cell and are crucial to it's survival.
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Extracellular matrix
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Which element has a unique atomic weight and why?
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Hydrogen...weight of only 1 because it has no neutron!
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the INNER (cytosolic) membrane of the lipid bilayer contains this Important phospholipid......
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PhosphatidyLINOSITOL
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the OUTER membrane of the lipid bilayer contains this important phospholipid......
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PhosphatidylCHOLINE
|
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This enzyme helps transfer phospholipids to the other half of bilayer to balance cell membrane...
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flippase
*It FLIPS! |
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chemical property of having a hydrophyllic carboxylic head and a hydrophobic hydrocarbon tail?
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amphipathy
(or having both polar and non-polar properties) |
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the hydrophyllic head of a phospholipid is made of _____.
|
polar group, such as choline or inositol
and a phosphate |
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a fat in which all covalent bonds are used up by hydrogens?
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saturated
|
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a fat in which there are fewer hydrogens, causing the molecule to kink?
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unsaturated
|
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basic structure of a lipid?
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fatty acids (hydrocarbon chain)
+ glycerol backbone |
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Isoprenoid
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lipids with multiples of isoprene in the form of (C5H8)n
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What are 2 examples of molecules made from isoprene (a lipid) units?
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Steroids & |
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lipid derivative with a carbohydrate attached?
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glycolipids
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a fat soluble enzyme which digests, transports and processes stored lipids for use within the body?
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lipase
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what are the 4 main biological functions of lipids?
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1. Structure of membranes
2. energy storage 3. essential vitamins (A, D, E & K) 4. Cell signaling |
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fats vs carbs: kcal per gram?
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carbs: 4 kcal
fats: 9 kcal |
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where are vitamins A,D,E,& K stored?
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liver, fatty tissues
|
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4 fat soluble vitamins that are isoprene based?
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A,D,E & K
(stored in liver and fatty tissues) |
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3 components of a phospholipid?
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1. Hydrophyllic head: polar group (like choline on outer or Inositol on inner) + phosphate
2. Linker: glycerol 3. Hydrophobic tail: fatty acids |
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how thick is the lipid bilayer?
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5 nm
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Surface of cell membrane is____.
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fluid.
lateral diffusion, flexion, rotation, and flip- |
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Where are phospholipids synthesized?
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endoplasmic reticulum
* Then new phospholipids are added to the cytosolic side of cell membrane. |
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what effect does cholesterol have on a cell membrane?
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stiffens it.
|
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what are the 4 main types of membrane proteins?
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1. transporters
2. anchors 3. receptors 4. enzymes |
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function of transporter proteins in membrane?
(example) |
Eg: Na+ pump
pumps sodium out and potassium in. |
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function of anchor proteins in membrane?
(example) |
eg. integrins
link intracellular actin filaments to extracellular matrix |
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function of receptor proteins in membrane?
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transmit growth signals
(for example, by binding an extracellular molecule) |
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function of enzyme proteins in membrane?
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eg. use extracellular signal to begin production of intracellular molcules |
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membrane proteins with oligosaccarides?
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glycoproteins
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membrane proteins with polysaccharides?
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proteoglycans
|
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The meshwork of fibrous proteins attached to the CYTOSOLIC surface of the membrane?
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Cell cortex
|
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the major component of the cell cortex.
Long thin flexible rod proteins about 10 nm long. |
Spectrin
|
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How are membrane proteins arranged within the cell membrane??
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locally confined, forming functionally specialized regions
|
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in what ways do cells create membrane domains (4)
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cell cortex
extra-cellular marix proteins of another cell diffusion barrier (tight junction) |
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What do we call the tight junction that cells form?
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diffusion barrier
|
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How are intestinal epithelial cells unique?
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they forms distinct apical and baso-lateral membrane domains.
|
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what are small amphipathic molecules called?
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detergents
|
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what are the two most common detergents we need to know?
|
SDS (sodium dodecyl sulfate, but call it SDS)
and Triton X-100 (number indicates strength) |
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basic structure of an amino acid?
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4 parts: -amino (NH) |
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what is an R group?
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side chain of an amino acid
|
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dehydration forms
___________ to link amino acids. |
peptide bonds
|
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what are the types of bonds that give proteins their 3D structure? (5)
|
1. ionic bonds(between CHARGED amino acids)
2. Hydrogen (with N or O or NH) 3. Van der Waals 4. hydrophobic (attract other hydrophobic) 5. covalent (between sulfurs) |
|
a covalent bond between 2 sulfurs in protein structure?
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disulfide bridge
|
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levels of protein structure:
the amino acid sequences. |
primary structure
|
|
levels of protein structure:
alpha helix or beta sheet |
secondary structure
|
|
levels of protein structure:
combination of alpha helices and beta sheets (eg. a-b-a) |
motif
(a motif of secondary structures) |
|
levels of protein structure:
final folded shape of a polypeptide (protein unit) |
tertiary structure
|
|
levels of protein structure:
a combination of multiple protein units. |
quaternary structure
|
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a segment of a polypeptide chain (protein) which forms a compact stable structure and ysually carries out a function. (usually enzymatic)
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Domain
|
|
another word for a polypeptide chain?
|
protein
|
|
amino acid represented by
D |
Aspartic Acid
Asp negative side chain |
|
amino acid represented by
E |
Glutamic Acid
Glu negative sidechain |
|
amino acid represented by
R |
Arginine
Arg positive side chain |
|
amino acid represented by
K |
Lysine
Lys positive side chain |
|
amino acid represented by
H |
Histidine
His positive side chain |
|
amino acid represented by
N |
Asparagine
|
|
amino acid represented by
Q |
Glutamine
Gln Uncharged polar side chain |
|
amino acid represented by
S |
Serine
Ser Uncharged polar side chain |
|
amino acid represented by
T |
Threonine
Thr Uncharged polar side chain |
|
amino acid represented by
Y |
Tyrosine
Tyr Uncharged polar side chain |
|
amino acid represented by
A |
Alanine
Ala nonpolar side chain |
|
amino acid represented by
G |
Glycine
Gly nonpolar side chain |
|
amino acid represented by
V |
Valine
Val nonpolar side chain |
|
amino acid represented by
L |
Leucine
L nonpolar side chain |
|
amino acid represented by
I |
Isoleocine
Ile nonpolar side chain |
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amino acid represented by
P |
Proline
Pro nonpolar side chain |
|
amino acid represented by
F |
Phenylalanine
Phe nonpolar side chain |
|
amino acid represented by
M |
Methionine
Met nonpolar side chain |
|
amino acid represented by
W |
Tryptophan
Trp nonpolar side chain |
|
amino acid represented by
C |
Cysteine
Cys nonpolar side chain |
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Amino acids with negative side chains?
|
Asparitic acid/ asp/ D
Glutamic acid / Glu/ E DE acids. |
|
Amino acids with positive side chains?
|
Arginine /Arg /R
Lysine/ Lys/ K Histidine/ His/ H |
|
amino letters which don't make sense...
|
Dasp (-)
gluE (-) Rarg (+) lysK (+) asnN Ytyr Wtrp Qgln |
|
differences between negative "acids" and the uncharged polar abbreviations for
aspartic acid vs asparagine and glutamic acid vs glutamine |
acids: first 3 letters (asp, glu)
uncharged polar: first 2 letters +n.(asn, gln) *Asn, Gln, Ile (Isoleocine) & Trp (tryptophan) are the ONLY abbreviations that don't start with the first 3 letters! |
|
How many nonpolar side chains?
|
10...that's half.
|
|
how many uncharged polar side chains?
|
5... a quarter of them.
|
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How many basic and acidic side chains?
|
3 basic (Arg, Lys & His)
2 acidic (Asp & Glu) |
|
C. elegans:
sexes and ratio of sexes? |
most are hermaphroditic
1 in 500 are male |
|
C. elegans:
Life cycle and lifespan? *important to differentiate! |
life cycle: 3 days
life span: 3 weeks |
|
C. elegans vocab:
Dauer |
larva goes into a type of stasis and can survive harsh conditions
(can be over 6 months) |
|
C. elegans: reasons they're good for genetic research?
|
Dauer (stasis) makes it low maintenence.
-genome is sequenced -short life cycle - we can manipulate it for lonegevity, cell structure, etc. |
|
Power and benefit of a dissecting microscope?
|
6.3X to 30X magnification
large working space for dissection. |
|
C. elegans vocab:
oviduct |
one of a pair of ducts through which eggs travel from ovary to uterus.
(formerly fallopian tubes) |
|
C. elegans vocab:
oocyte |
immature egg of all animals and some protists
|
|
C. elegans vocab:
cloaca |
chamber or duct in last portion of gut of some animals that serves in excretion, reproduction and sometimes respiration
|
|
C. elegans vocab:
spicule |
a small hard needle-like piece of bony material, as in the skeleton of a sponge.
|
|
C. elegans vocab:
alimentary canal |
the passage in the body through which food passes as it's digested. from mouth to anus. aka: digestive tract?
|
|
4 functions of extracellular proteins?
|
1. structure (eg. collagen)
2. enzymes (eg. lysozyme) 3. growth factor (Fibroblast growth factor) 4. immune response (antibodies) |
|
4 functions of membrane proteins?
|
1. transporters, e.g. __ion channels__
2. anchors, e.g. __integrins___ 3. receptors, e.g. growth factor receptors 4. enzymes, e.g. adenylyl cyclase coverts extracellular molecule to an intracellular messenger. 5. recognition, e.g. _glycoproteins___ |
|
6 Functions of intracellular proteins?
|
1. enzymes, e.g. _kinases__
2. structural proteins, e.g. actin filaments, spectrin 3. motor proteins, e.g. myosin 4. receptors, e.g. __hormone receptors__ 5. signal transduction 6. special functions, e.g. _DNA bind proteins__ involved in replication, transcription, translation |
|
enzymes are always made of _____.
|
proteins
|
|
Where do enzymes serve functions?
|
in cell, in membrane and extracellular
|
|
what are growth factor proteins?
|
these are extra cellular proteins like FGF (fibroblast growth factor) that bind with a receptor protein in the cell membrane that in turn alters intracellular molecules creating a response.
|
|
How do membrane recognition proteins function?
|
Recognition proteins are usually glycoproteins with the carbohydrate portion projecting out of the cell and into the extracellular space. These give the cell a biochemical personality (like ID) and are important in cell-to-cell recognition.
|
|
How do membrane enzymes function?
|
they convert extracellular molecules to intracellular messengers.
|
|
what is ligase?
|
a DNA binding protein (special function intracellular protein)
binds 2 strands of DNA together end to end. It is an enzyme. |
|
chaperones (molecular):
What do they do and where are they found? |
molecules that assist in protein folding
ER |
|
Where are motor proteins found?
|
intracellular!
(move along microtubule substrate) |
|
Where are structural proteins found?
|
intra & extra cellular
(collagen, actin, etc) |
|
where are receptor proteins found?
|
membrane and intracellular
|
|
signal transduction?
|
the process by which a cell responds to an extracellular signal
|
|
Where are signal transduction proteins found?
|
intracellular
|
|
What connects elastin fibers?
|
"cross links" = covalent bonds
|
|
What are the "Special functions" performed by some intracellular proteins?
|
transcription, translation, RNA modification, etc
|
|
fibrous proteins that are a major component of the extracellular matrix and connective tissues?
|
collagen & elastin
|
|
what are the side effects of protein denaturing?
|
lose function, cause disease
|
|
special mis-folded proteins that cause scapie, mad cow, sickle cell anemia?
|
Prion
|
|
the region where an enzyme interacts with another molecule?
|
active or binding site
|
|
how do protein aggregates form?
|
a misfolded protein converts normal Prp to abnormal conformation creating aggregates.
|
|
PrP?
|
prion proteins
|
|
The place on an enzyme where a molecule that is not a substrate may bind, important for conformation.
|
allosteric site
|
|
allosteric site?
|
The place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme and influencing its ability to be active. (proper conformation)
|
|
Enzymes, receptor and antigens: what does each interact with?
|
enzyme- substrate
receptor- ligand antibody- antigen |
|
What is immunuglobulin?
|
antibodies
|
|
shape of antibody/ immunoglobulin?
|
Y shaped
|
|
what gives antibodies their Y shape?
|
many intra and inter molecular S-S (disulfide) bonds
|
|
a domain of an antibody that binds a specific antigen?
|
variable domain
|
|
Why is an antibody called a tetramer?
|
4 parts: composed of two heavy and two light chains.
|
|
technique to separate proteins by charge, size, affinity to other substances or proteins using specific solutions
(matrices)? |
Chromoatography
|
|
technique to separate proteins by their molecular weight (and net charge)?
|
electrophoresis ,
including the now obsolete SDS |
|
technique that separates denatured proteins by isoelectric point and then by molecular weight.
|
Two-dimensional gel electrophoresis
|
|
technique which obtains high resolution image of crystal structure of proteins?
|
X-ray crystallography
|
|
basic description of X-ray crystallography
|
beam of x rays through protein crystals, then they obtain a diffraction pattern which they convert to computer image.
|
|
generates a 3-D structure (like x-ray crystallography) but with lower resolution
|
NMR spectroscopy
|
|
extracellular (ECM)
vs intracellular proteins (cytoskeleton) |
extra: collagen and elastin
intra: spectrin and actin |
|
what are integrins?
|
membrane anchor proteins
|
|
where are antibodies located?
|
extracellular
|
|
example of a proteoglycan?
|
chondroitin sulfate , a structural component of cartilage
|