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218 Cards in this Set
- Front
- Back
What does cytology focus on? |
Focuses on cellular structure and uses optical techniques |
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Biochemistry focus: ? |
Focuses on cellular function |
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Genetics focus : ? |
Focuses on information flow and genetics
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What are two tools used by cytologists? (3) |
•Themicrotome-- Allows the preparation of very thin slices of samples •A variety of dyesand the development of immunohistochemistrytechniques -- Stain cells or cell compartments/molecules •The smaller the limit of resolutiona microscope has, the greater its resolvingpower |
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electron microscope stats: |
resolving power 0.1-0.2 nm 100 000x magnification |
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Tools used in Biochemistry (3): |
•RadioactiveIsotopes-- to trace the fate of specific atoms and molecules •Subcellularfractionation -- suchas centrifugationto separate/isolate different structures and macromolecules •Ultracentrifuges--capable of very high speeds (over 100,000 revolutions per minute) |
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Tools used in Biochem pt.2 (3): |
•Chromatography--Separates molecules from a solution based on size, charge, or chemical affinity••Electrophoresis--Uses an electrical field to move proteins, DNA or RNA molecules through amedium based on size/charge••MassSpectrometry --Determines the size and composition of individual proteins |
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Origin of genetics? Chromosone Theory of genetics come from this work |
Gregor Mendel's Pea experiment in 1866. Described hereditary factors. Now known as genes. - Chromosome Theory of Genetics would come from his work and others |
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Each gene is responsible for : ? |
A single protein |
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Who proposed the DNA double helix? |
Watson and Crick in 1953 |
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What are two tools used in genetics that Separates DNA and RNA molecules: ? |
Ultracentrifugation and electrophoresis
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What is a tool used in genetics that Uses the ability of nucleic acid bases to bind to each other? |
Nucleic acid hybridization |
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What is the technology used in genetics that uses Restriction enzymes to cut DNA at specific places forming recombinant DNA molecules,with DNA from different sources? |
Recombinant DNA technology
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What is a tool used in genetics to rapidly determine the base sequencesof DNA molecules? |
DNA sequencing |
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In vitro is? |
•using purified chemicals and cellular components |
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In vivo is? |
•using live cells or organisms |
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Insilico is ? |
• using computer analysis of largeamounts of data |
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Define Hypothesis |
statement consistent with most of the data, may take the form of a model(an explanation that appears to account for the data); must be testable |
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Define a Theory: |
a hypothesis that has been extensivelytested by many investigators, using different approaches, widely accepted |
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Define a Law: |
•atheory that has been tested and confirmed over a long period of time withvirtually no doubt of its validity |
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Lecture 2. The Chemistry of the cell. |
YAY! |
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What are the five principles of Cell biology? |
--Characteristics of carbon and water. -Selectively permeable membranes –Synthesis by polymerization of small molecules Self Assembly |
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Which 5 other atoms is carbon most likely to bind to ? |
PHONS. |
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What is stability expressed as? |
Bond energy - theamount of energy required to break 1 mole (~6x 1023) of bonds |
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•Bond energy is expressed as caloriesper mole (cal/mol)•Acalorie isthe amount of energy needed to raise the temperature of 1g of water by 1oC |
:P |
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Which functional groups are negatively charged?
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Carboxyl and phosphate |
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Which are positively?
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amino
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Which are (uncharged;but polar) ?
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Hydroxyl, sulfhydroxyl, carbonyl, aldehyde |
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What is a configurational stereoisomer? |
A non superimposable mirror image ( chiral) |
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A compound with nasymmetric carbons willhave how many possible stereoisomers? |
2^n. Each asym C has two possible stereoisomers. |
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What is responsible for the high: Surfacetension, Boilingpoint and Heatof vaporization of water? |
The extensive network of Hydrogen bonding |
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How does water absorb so much heat with little change in temperature? |
Heat is absorbed by breaking the many hydrogen bonds |
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What is heat of Vaporization? |
•the amount of energy required to convert one gram of liquid into vapor |
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The high heat of vaporization of water makes it an excellent solvent for cells. Why? |
B/c it protects proteins in solution from overheating
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How do water molecules reduce the chances of re-association between dissolved ions? |
They form spheres of hydration around the ions |
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Cell membrane consists of ? (3) + 3 |
phospholipids, glycolipids and membrane proteins. Also sterols. cholesterol in animals •ergosterols (fungi), or phytosterols (plants) |
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What are the main 3 types of membrane proteins? |
Transport Enzyme Receptor |
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Are membranes permeable to polar or nonpolar molecules?
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Non polar because of the hydrophobic interiors
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Why are even the smallest of Ions still unable to diffuse across the bilayer? |
Because of their charge and the surrounding hydration shell. |
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Consider revising types of transports proteins. 7 in total |
:P |
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In the polymerization of monomers, monomers must first be _______ before condensation can occur? |
activated. Once activated it is in a higher energy state, and it consumes this energy during condensation sythesis |
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How does a monomer become activated? |
Is must be coupled with a carrier molecule |
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Does this process use ATP? |
Yes, or an alternative high E molec. |
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Remember that the carrier molecule is removed after condensation. |
:P
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What is the carrier molecule of protein synthesis?
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tRNA |
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What is the carrier molecule of Polysaccharide synthesis? |
sugars (monomer) are often activated by linking them with ADP and UDP. |
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What is the carrier molecule of Nucleic Acid synthesis? |
–nucleotides themselves are high-energymolecules (ATP, GTP) |
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Assisted self-assembly has what? |
molecular chaperones
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What class are many chaperones a part of ? |
Heat shock |
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What are two advantages to heirarchical self assembly, in terms of simplicity and efficiency? |
relatively few subunits are used for a wide variety of structures a small number of condensation reactions are needed |
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What is another advantage in terms of quality control? |
Early mistakes can be repaired or omitted before being incorporated into larger structures |
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There are 8 types of proteins. The follow are the less obvious ones |
Lets get em |
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Structural Proteins |
-- physical support and shape (e.g., cytoskeletal proteins) |
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Motility Proteins |
-- contraction and movement (e.g., muscle proteins: myosin & actin) |
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Regulatory Proteins |
control and coordinate cell function (e.g., cell signaling, cell death, gene transcription/repression) |
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Transport Proteins |
move substances in and out of cells (e.g., membrane transporters and channels) |
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Communication Proteins |
communication between cells (e.g., hormones, neurotransmitters) |
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Receptor Proteins |
enable cells to respond to chemical stimuli from the environment |
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Defensive Proteins |
Defensive Proteins |
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Storage proteins -
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reservoirs of amino acids
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All proteins are made from the same 20 amino acids. But some do not. What is this the result of? |
Modification |
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9 AA have unpolar hydrophobic groups |
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What are the two acidic AAs? |
Aspartate and glutamate Asp and Glu GluAsp |
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What are the three basic AAs? |
Lys Arg and His LAH |
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Describe a peptide bond? |
C-N covelent bond b/w two AAs |
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Two cystein residues may form which type of bond? |
covalent disulfide bonds |
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How are the formed? |
With the removal of two hydrogens. (Oxidation) |
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Are these bonds intermolecular |
Yes, but also intramolecular |
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Polypeptides form in which direction? |
N-terminus --> C-terminus |
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Which bonds and forces maintain quaternary structure? |
The same as tertiary. H bond van der waals ionic hydrophobic covalent (s-s) |
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What are the two Purine bases? |
Adenine and guanosine A and G |
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What are the Pyrmidines? |
Thymine, cytosine and uracil |
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What is a sugar base portion of DNA? |
A nucleoside |
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A nucleside + ________ = nucleotide? |
Phosphate |
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What is the difference in the sugar b/w DNA and RNA? |
DNA 2' C-H RNA 2' C-OH |
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Adenine forms __ H-bonds with __? |
2,Thymine
Uracil if RNA |
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Cytosine forms __H-bonds with ___ ? |
3 H - bonds with Guanine |
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Polysaccharides consist of ____ repeating unit(s) |
1 sometimes two in alternating fashion |
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What is the most common sugar?
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aldohexose. D-glucose, which is the most stable stereoisomer
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In the cell does D-glucose exist as a ring? |
No. It exists in an equilibrium b/w linear and ring form. Fisher projection shows linear form and makes aldehyde obvious |
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How is alpha D glucose defined? |
In alpha D glucose the 1 C OH group is downwards |
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How is beta D glucose defined?
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In beta D glucose the 1C OH group is upwards |
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What type of bond links disaccharides? |
glycosidic bonds (with the elimination of water) |
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Glycosidic bonds involving A-D-glucose are called glycosidic bonds |
Glycosidic bonds involving B-D-glucose are called B glycosidic bonds |
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if a A-D-glucose bonds with a B-D-Fructose, what type of bond will form? |
an A-glycosidic bond |
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The most common storage polysaccharide in animals is? |
glycogen |
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The most common storage polysaccharide in plants is ? |
Starch |
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How would one describe the bonding of starch and glycogen ? |
A 1-->4 glycosidic With branching at A(1--->6) |
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How often does glycogen branching occur? |
Every 8-10 glucose units |
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Where is glycogen stored in animals? |
In liver, for glucose, and in muscle as a fuel source for muscle contraction |
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In what two forms does starch occur? |
As branched (every 12-25 glucoses) Amylopectin (70-90%) and amylose (10-30%) |
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Where is starch stored? |
In the plastids as starch grains. In amyloplasts and in chloroplats |
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What is the compositon of cellulose? |
B-D-Glucose |
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Bacterial cell walls contain which two kinds of sugars?
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GlcNAc (N-acetylglucosamine) and MurNAc (N-acetylmuramic acid) |
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And they are derivatives of what? |
B-glucosamine, |
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Linked alternately with what type of bond? |
B(1--->4) |
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What is chitin's composition? |
GlcNAc, B (1--->4) |
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Polysaccharide Structure Depends on the Type of Glycosidic Bonds Involved
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Sure does.
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A-glycosidic are loose |
B-glycosidic are rigid linear rods that aggregate into microfibrils, about 5-20 nm in diameter |
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Lipids
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yay! |
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What are 3 functions of lipids? |
energy storage, membrane structure and signal transmission |
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few polar groups, but some are amphipathic, with polar and nonpolar regions |
ya |
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There are 6 classes of lipids |
un mas |
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What is the structure of a fatty acid? |
Long unbranched hydrocarbon with a carboxyl group at one end |
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12 to 20 carbonsEven numbers of carbons are favored because fatty acid synthesis occurs via the stepwise addition of two-carbon units |
Fatty acids are highly reduced and generate a large amount of energy upon oxidation |
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What are 2 functions of triaglycerols? |
Energy storage and insullation |
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Animals triacylglycerols are semi solid at room temp |
Plant TGCs are fluids. They are predominantly unsaturated fatty acids |
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What are two types of phospholipids?
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Phosphoglycerides and sphingolipids |
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Draw a phosphatic acid. Which is the backbone of phosphoglycerides, which are the predominant phospholipid in membranes |
2 fatty acids and a phosphate group attached to a glycerol |
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The R group is usually serine, ethanolamine, choline, or inositol, which contributes to the polar nature of the phospholipid head group
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Usually have 1 sat and 1 unsat tail
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Where are sphingolipids found? |
On the outer leaflet of the plasma membrane |
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What are glycolipids? |
Lipids with a carbohydrate group instead of a phosphate group |
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What are they derived from? |
Glycerol and sphingosine |
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Carb group 1-6 sugars long
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Occur largely on the outer monolayer of the plasma membrane |
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What is the base structure of steroids? |
tetracyclic hydrocarbon |
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Are they polar? |
No, they arn't |
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How do they differ from one another? |
Functional groups and location of double bonds |
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Whats the most common steroid in animals? |
Cholesterol, it plays a large role in membrane fluidity |
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What is cholesterol the precursor of?
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Steroid hormones. Such as M and F sex hormones, glucocorticoids and mineralcorticoids |
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What are estrogens and androgens? |
Female SH and male SH |
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What do glucocorticoids do? |
they promote glucosneogenesis and reduce inflammation |
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What do mineralcorticoids do? |
They promote reabsorption of HCO3-, Na, and Cl by the kidneys |
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What are terpenes synthesised from? |
Isoprene, a 5 C compound |
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Terpenes and its derivatives are joined in various combinations to produce substances such as____? |
Vitamin A and Cartenoid pigments |
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While archaea and bacteria are both prokaryotes, rRNA sequence analysis reveals how widely divergent archaea are from bacteria |
:P |
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Where are archaea commonly found? |
In extreme condition where they have developed diverse metabolic strategies |
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What are methanogens?
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Archaea who get energy from H2 and convert CO2 into methane
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What are Halophiles |
Archaea who occupy extremly salty environments
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What are Thermacidophiles? |
Archaea who live in acidic hot springs |
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Archaea emerged from a common ancestor of eukaryotes long after diverging from bbacteria |
ya! |
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Cells are small because? |
Beyond a certain threshold they would not be able to take in enough nutrients and release enough wastes |
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Many molecules rely on diffusion to move around the cell. Larger molecules have a slower rate of diffusion. |
>.>
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What are some steps cells take to avoid the limitations of diffusion? |
Carrier proteins to actively transport materials through the cytoplasm. And vesicles transported along microtubules |
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Cells must also stay small because of the necessity to maintain adequate reactant and enzyme concentrations, so as to maintain a high level of collisions b/w reactants and enzymes |
yay! |
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As cell size increases the number of molecules must increase proportionate to__________?
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Cell volume, which grows a lot |
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How do organelles avoid the issue of concentraions? |
They are specialized compartments for specific functions |
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The nucleolus, which is a distinguishing feature of eukaryotes from prokaryotes, also is the site of what synthesis and assembly? |
rRNA synthesis and ribosome assembly |
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Eukaryotes have a nuclear membrane, which has 2 membranes. How is bacterial DNA arranged? |
the genetic information is folded into a compact structure called the nucleoid and is attached to the cell membrane |
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How is bacterial DNA organized? |
Circular with few protein interactions |
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How is EUK DNA organized? |
linear and complexed with large amount of histones |
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How is Archaea DNA organized |
circular and complexes with proteins similar to EUK histones |
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Bacterial and Archaeal cell duplicate their DNA and divide by ________? |
binar fission |
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Eukaryotic cells replicate DNA and distribute their chromosomes into daughter cells by mitosis & meiosis, followed by cytokinesis, division of the cytoplasm |
:PPP |
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This type of cell transcribes genetic information into RNA, and each RNA molecule may contain information for several polypeptides. What type is it ? |
Bacterial |
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RNA molecules become involved in protein synthesis before transcription is complete. What type of cell does this? |
Archaea and Bacteria |
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CMMMMembrane ! |
woop woop |
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What type of proteins would the cytoskelton connect to in the plasma membrane?
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Anchor Proteins |
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Nucleopores are lined with what complex? |
nuclear pore |
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When are chromosomes most visible? |
During mitosis |
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When are chromosomes least visible? and what form are they in during said phase |
During interphase when they are dispersed as chromatin |
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Mitochondria contain small circular molecules of DNA, which encodes some RNAs & proteins needed for mitochondrial function |
yup |
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Mitochondria also have their own_________ to carry out protein synthesis? |
ribosomes |
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How is ATP produced in the mitochondria?
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By the oxidation of sugars and other fuel
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What are the cristae of the mitochondria? |
infoldings of the inner mitochondrial membrane |
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What is the mitochondrial matrix? |
The fluid that fills the inside of the mitochondrion |
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Where are most proteins of the mitochondria localized? |
The cristae and the matrix |
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Tissues with high demand for ATP have many mitochondria, located within the cell at the site of greatest energy needsE.g.: sperm cells |
---------_-_-_> also e.g. muscle cells
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Chloroplasts and Mitochondria are surrounded by both ________ and ____________ membranes? |
inner and outer |
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Chloroplasts contain a system of __________ that are stacked into __________ |
thylakoids stacked into grana |
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In or on thylakoid membranes are the site of what reactions? |
Solar energy dependant reactions |
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Reactions involved in the reduction of CO2 to sugar occur within the__________ |
stroma, which is asemifluid in the interior of the chloroplast |
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Chloroplasts also reduce NO3- from soils into __________
(hint: is it needed for protein synthesis) |
NH3 |
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Chloroplast function is the reverse of mitochondrial reactions that __________ glucose into CO2
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oxidize |
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How do chloroplasts relate to mitochondria?
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They have a small amount of circular DNA which codes for a few of their own ribosomes and proteins
DNA not associated with histones |
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The inner membrane of MIT and CHLO has what type of lipids? |
Bacterial lipids |
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tubular membranes and flattened sacs of the ER are called what?
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cisternae
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The internal space of the ER is the |
lumen |
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The ER is continuous with other parts of the cell |
OK! |
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The RER is studded with _____________ and their role is ____________? |
ribosomes that synthesize polypeptides |
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Where do those polypeptides go? |
Either the accumulate in the membrane or are transported to the lumen |
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What is the role of the SER |
Lipids synthesis e.g. cholesterol and its derivatives |
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It is also responsible for __________ and ___________ harmful substances? |
deactivating and detoxifying |
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Sarcoplasmic reticulum does what ? |
sequesters Ca2+ ions critical for contraction tissues |
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What is the main function of the GA ? |
processing & packaging secretory & membrane proteins |
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What is another, similar role of the GA? |
complex polysaccharide synthesis |
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It also accepts __________ that bud off from the _________ |
vesicles ER |
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Secretory and membrane proteins are often glycosylated. Where does this occur? |
It begins in the ER and then is completed in the GA |
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How do these processed materials move to other parts of the cell? |
In vesicles that bud off the GA |
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Exocytosis releases contents into the ECM
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hey ho |
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What are the 4 components that constitute the endomembrane system, which trafficks substances through the cell |
ER, GA, vesicles and lysosomes |
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What do lysosomes store? |
Hydrolases |
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What are hydrolases? |
enzymes that can digest any kind of biological molecule |
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How is the lysosome protected from the hydrolases that it sequesters? |
A special carbohydrate coating |
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How is H2O2, a harmful by-product of cellular respiration managed within the cell? |
H202 is converted into H20 and 02 by catalse enzyme which is present in peroxisomes |
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What else do peroxisomes do? (hint: related to SER) |
detoxify toxins |
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Where in the body are peroxisomes found in high concentration? |
Liver and kidneys |
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What is the role of vacuoles in animal and yeast cells? |
Temporary storage or transport |
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A phagosome is the result of __________? |
phagocytosis |
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If a phagosome (vacuole) fuses with a lysosome its contents are _____________to provide _____________ for the cell |
hydrolyzed nutrients |
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Why are ribosomes not organelles? |
B/c they are not enclosed by a membrane |
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They are found in all cells but differ in bacteria, archaea and eukarya in their size & composition |
nice |
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EUK cell ribosome sediment coefficients are approx ? |
60s and 40s |
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50s and 30s in _________ and ___________ ? |
Bacteria and Archaea |
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Other than structural support, what are 3 roles of the cytoskeleton? |
Cell division Cell movement Intracellular transport |
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What are the largest structural elements of the cytoskeleton |
microtubules |
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mitotic spindle fibers and axoneme of cilia are both _____________ based structures? |
microtubule |
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draw and label a microtubule and its monomers
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do it
Atub+Btub= tubulin dimer --> protofilament --> microtubule |
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What are the smallest components of the cytoskeleton |
microfilaments? |
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What is the monomer of mircofilaments? |
Actin |
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Draw and label a microfilament and its monomers |
Microfilaments Are polymers of the protein actin Actin is synthesized as a monomer called G-actin (globular) These subunits are polymerized into F-actin (filamentous), with a helical appearance G-actin ---> F-actin ----> Microfilament |
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These filaments are the most stable and least soluble. What are they? |
Intermediate filaments |
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Where are they found |
Areas of mechanical stress such as muscle cells |
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There are six classes of intermediate filaments and animal cells from different tissues can be distinguished on the basis of the types of intermediate filament proteins they contain |
just stop |
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Animal cell ECM consists of _______ fibers and ___________ |
collagen and proteoglycans |
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What is role of proteoglycans? |
They confer mobility and elasticity
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What does the primary cell wall consist mainly of ? |
Cellulose fibrils embedded in a polysaccharide matrix
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Secondary Cell Wall: Formed once the cell reaches its final size & shape by ?
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deposition of additional cellulose and pectin on the inner surface of the primary cell wall
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How are plant cells connected? |
Plasmodesmata |
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How large molecules can pass through plasmodesmata? |
H2O and small solutes |
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How do animal cells communicate? |
Gap junctions. Tight and adhesion jctns also connect animal cells |
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Viruses are noncellular parasitic particles incapable of _________________________?
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Free living existence |
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consist of only a few different molecules of____________? |
nucleic acid and protein |
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they use invaded cells' machinery to produce more virus particles |
uh oh |
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Viruses consist of a ____________ (protein coat) that encapsulates a core containing _______ and ______ |
capsid DNA RNA |
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Enveloped viruses are ones that _________ |
are surrounded by a membrane |
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Viruses have no ________, _________ and can only reproduce via the machinery of other cells |
metabolism irritability ( ability to perceive and respond to outside stimuli) |
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Asymetric carbons allow for the formation of ________ which are mirror images of eachother |
configurational stereoisomers |
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Which of thefollowing can only be viewed by electron microscopy? A) Frog eggs B) Viruses C) Nuclei D) Mitochondria E) Bacteria |
B) |