Term
what is the primary function of membranes?
Other functions (5) |
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Definition
Boundry!
prevents loss of metabolites
prevents unwanted shit from getting in
transports nutrients in and wastes out
maintains ionic composition
provides a surface |
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Term
| 2 processes that occur in the nucleus |
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Definition
| DNA replication, RNA transcription |
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Term
| where does protien translation and transport mostly occur? |
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Definition
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Term
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Definition
| protease, nuclease (cuts protien and nucleaic acids) |
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Term
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Definition
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Term
| What does amphipathic phospholipid mean? |
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Definition
DUAL SYMPATHY
polar head group, non polar tail |
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Term
| how long is the tail in a typical amphipathic phospholipid? |
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Definition
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Term
| this phospholipid is the precursor to most of the other ones |
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Definition
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Term
| Describe what hapens to lipids in water |
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Definition
they form an ordered monolayer
As the concentration is raised, they either form micelles (Micelle concentration limit) or Bilayers, no limit to their size |
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Term
| What allows cell membranes to have a dynamic interaction with their enviroment? |
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Definition
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Term
| Who came up with the fluid mosaic model and when? |
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Definition
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Term
| Explain the Frye-Edidin Experiment |
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Definition
| Fused 2 cells with different antigens. After a while mixing was obsurved |
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Term
| How do peripheral proteins interact with the membrane? |
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Definition
| electrostatic and hydrogen bonding with INTEGRAL proteins |
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Term
| how might we dissociate interactions between peripheral proteins and integral proteins? |
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Definition
| disrupt interactions (with Salt, EDTA, urea etc) |
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Term
| How do lipid anchored proteins interact with the membrane? |
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Definition
plop a lipid "anchor" into the bilayer
that process is called lipidation |
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Term
Describe the AAs involved with the following lipidation events:
1)myristoylation
2)prenylation
3)Palmitoylation |
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Definition
1) glycine
2) cystine
3)cystine |
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Term
| how might we extract integral protiens from the membrane? |
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Definition
| detergents (organic solvents) |
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Term
| 2 different classifications of detergents |
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Definition
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Term
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Definition
| critical micelle concentration |
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Term
| Name 4 integral membrane protiens and their functions |
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Definition
| 1) Glycophorin, dictates ABO and MN blood type (receptor for flu virus) 2) Histamine (H1) receptors. Bind with histamine and mediate the allergic response 3) ATP synthase, generate ATP 4)Polycystin-1, regulate entrance of Ca++ into cell |
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Term
| genetic basis of Cystic Fibrosis? |
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Definition
| leads to abnormal Cl- membrane permeablility resulting in increase viscosity of body secretions (DEATH!) |
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Term
| How doyes Cyanide poisioning work? |
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Definition
| binds to cytochrome a3, prventing movment of H+ across mitochondrial membrane. Oxidative phosphorylation cant continue |
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Term
| How does polycystic kidney disease work? |
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Definition
Mutation of polycistin (-1 or -2). Disrupts ca++ entrance, increased cellular proliferation and fluid secretion
Ca cant inhibit braf |
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Term
| what does rattlesnake venom do? |
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Definition
| contanins a phospholipase which hydrolizes glycerophospholipids. ONe of the products (lysolecithin) acts as a detergent, disolving the membranes of erythrocytes |
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Term
| Describe the flow of genetic info |
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Definition
| DNA (replication)-->RNA(transcription)--->Protein(translation) |
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Term
Pyrimidies vs Purines
which are which?? |
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Definition
Pyrimidies are 6 member rings
purines are pyrimidies with a 5 member ring attached
Adenine and Guanine are purines
Cytosine Thyamine and Uracil are pyrimidines |
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Term
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Definition
Nucleoside is a base itself
Nucleotide is base + sugar + phosphate |
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Term
| how are the bonds between nucleotides formed? What are they called? |
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Definition
| 5'phosphate will bond with a 3' -OH to form a phosphodiester |
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Term
| which nucleotide bonds with what? How many bonds? What kind of bonds? |
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Definition
| A-T 2 H bonds, G-C, 3 bonds |
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Term
| Why do DNA strands run antiparallel, is this good or bad? |
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Definition
| they run antiparallel b/c the nucleotides twist to bond, this is good because one one strand can serve as a tamplate for the other one |
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Term
| in which direction does replication occur? |
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Definition
| 5' ---->3' always, no exceptions |
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Term
| How do we describe DNA synthisis? |
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Definition
| semi-conservative, keeps 1/2 the parant strand |
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Term
| In which phase of the cell cycle does DNA replication occur? |
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Definition
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Term
| Briefly describe replication |
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Definition
| dnaA binds, causeing "melting to occur. dnaC guides dnaB to the single stranded DNA then releases. Now uninhibited, dnaC (helicase) unwinds the DNA. dnaG (primase) binds and makes RNA primers. DNA polymerase then binds to the primer and begins replicating in the 5' --> 3' direction |
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Term
| How does DNA polymerase work? |
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Definition
| Catelyises the attach of the 3' OH to the 5' phosphate |
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Term
| What helps prevent supercoiling during replication? |
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Definition
| DNA gyrace breaks DNA down stream so all the kinks can come out, then reseals it |
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Term
How do fluoroquinolone abx work?
Name 2 drugs in this class |
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Definition
target DNA gyrase in gram neg bacteria
ciprofloxacin and levofloxacin |
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Term
| briefly describe how DNA polyemerase I, III and ligase work together, on which strand is this used? |
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Definition
pol 3 starts at the primer and runs to the next primer. pol 1 then attacks the primer, removing it while simultaneously inserting DNA (endonuclease), ligase catylizes the final 3-5 phosphodiester bonds between the strands (Ligase reguires ATP)
ON the lagging strand (leading strand will only need dna pol 3 for complete synthesis) |
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Term
| this protien prevents the DNA from reforming H bonds before replication occurs |
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Definition
| SSB (single stranded binding protein) |
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Term
| 4 kind of base pair mutations discussed in class |
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Definition
transition: pyrimidine to purimidine
transversion: pyrimidine to a purine
deletion
insertion |
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Term
| What is one of the most common causes of a mutation in DNA? |
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Definition
spontaneous mutation
One base is transformed into it's tautomeric counterpart (A-C go from amino to imino. G-T go from keto to enol
For example, imino cytosine will bind with Adenine, yikes! |
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Term
| 3 other ways that mutations can occur |
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Definition
| chemical mutagens, UV light (forms a cyclic butane, yikes!) |
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Term
primary repair mechanism for point mutations?
What about the ones that are missed by proofreading? |
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Definition
proofreading by polymerases
mismatch repair, then excision repair |
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Term
| How does the proofreading mechanism know which base is wrong on a missmatch? |
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Definition
| After all proofreading is done, certain adenine bases are methlyated, signaling a parent strand, the new strand isnt methylated until all proofreading is complete |
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Term
caused by mutations in genes involved in nucleotide excision repair
associated with a >1000-fold increase of sunlight-inducedskin cancer |
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Definition
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Term
caused by gene that detects DNA damage
increased risk of X-ray
associated with increased breast cancer in carriers |
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Definition
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Term
caused by mutations in a a DNA helicase gene
increased risk of X-ray
sensitivity to sunlight |
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Definition
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Term
caused by a defect in transcription-linked DNA repair
sensitivity to sunlight |
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Definition
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Term
caused by mutations in a DNA helicase gene
premature aging |
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Definition
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Term
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Definition
| Inherited mutation or Loss/Gain of function |
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Term
| whats the diff between DNA and RNA shapes? |
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Definition
| Ribose has a 2' hydroxyl that makes the 3',5' phosphodiester bond unstable |
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Term
| these are minimal elements required to franscription (burger and buns) |
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Definition
| General Transcription factiors and RNA polymeralse II |
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Term
| What are the 3 phases of the general transcription factors? What is the final result? |
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Definition
TFIID binds to TATA box and begins assemblu of the transcriotion aparatus
TBP (TATA binding protien) binds directly to the TATA box
TBP associated factors (TAFs) bind to it
the final result is a promotor for DNA polymerase II to bind to it |
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Term
| What is transactivation during transcription? |
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Definition
| transcription factors, bind to other promotor elements combind with other transcription elements interat with protiens at the promotor to further stablize or inhibit it |
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Term
| what determines the rate of initiation of transcription? |
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Definition
| the stability and frequencey of preinitiation complexes |
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Term
| What makes RNA pol II go from the preinitiation complex? |
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Definition
| its phosphorylated by TFIIH on the carboxy terminal domain. Thus releasing it and allowing elongation to continue |
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Term
| what do all eukaryotic RNAs have that prokaryotics dont? WHats the only exception? |
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Definition
a 5' cap and a poly (A) tail (during processing)
histone mRNAs dont have the cap |
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Term
| the basic types of amino acids |
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Definition
| non-polar, polar non charged, acidic, basic |
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Term
| describe a eukaryotic ribosome |
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Definition
| 60s subunit + 40s subunit = 80s subuint |
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Term
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Definition
| AP1 dimer protein binds to the palendrome sequence TGACTCA and acts as a TF. Jun (one of the subunit protiens) can be phosphorylated and further stimulate AP1's activity |
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Term
| when zinc fingers inserts a steriod into DNA, where to the fingers go? |
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Definition
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Term
| L-form of hemophilia vs B-form |
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Definition
Both deal with factor IX gene (for blood clotting)
L form is mutated at a place where the HNF4 TF cannot bind but the AR can. In the B form, the mutation is in a place where neither can bind |
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Term
| which direction does translation take place? |
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Definition
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Term
| how does the codon known where to begin? |
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Definition
| It starts at the first AUG codon following the 5' cap. It follows a Kozak sequence to the first start (AUG codon) |
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Term
| After the 40s subunit finds the first AUG, what happens next? |
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Definition
the eIF2 protien is ejected, and the 60s subunit binds
aminoacyl tRNA binds to the A-site and the first peptide bond is formed |
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Term
| 1 start codon, 3 stop codons |
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Definition
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Term
| How do codons and anticodons work? |
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Definition
| each tRNA is bound to a specific aminoacyl (an AA with ribose adenine on it). The bottom of the tRNA has an anticodon which bonds to the proper codon. |
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Term
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Definition
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Term
| one peptide bond forms, what next? |
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Definition
--uncharged trna ejected from p site --ribosomes shifts one codon and peptidyl trna is shifted from A to P site --EF1 brings next aminoacyl tRNA to the A site
--ef 2 pulls the chain along
(ef = elongation factor) |
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Term
| what provides energy for translation? |
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Definition
hydrolisis of 2 GTP
one for translocation, one for aminoacyl tRNA binding |
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Term
| what happens when translation reaches a stop codon? |
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Definition
RF binds to the A site catalizing the hydrolysis of the peptide from the tRNA.
the complex dissociates |
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Term
| why is a frameshift mutation devistating? |
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Definition
| codons come in 3s, the loss of one changes EVERYTHING (usualy) |
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Term
| Which 2 groups make the charged AAs? |
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Definition
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Term
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Definition
| Lysine, Arginine Histidie (barely) |
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Term
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Definition
| aspartic acid, glutamic acid |
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Term
name the uncharged polar AAs
(7) |
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Definition
| serine, tyrosine, threonine, cystine, glutamine, asparagine, glycine |
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Term
| which AA can form a sulfer bridge? |
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Definition
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Term
what are the non polar AAs?
(8) |
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Definition
| alanine, proline, leucine, isoleucine, valine, tryptophan,phenylalanine, methionine |
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Term
| what forms a peptinde bond? |
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Definition
| a condensation rxn between the carboxyl of one AA and the amino of another |
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Term
| How do van der walls forces work? |
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Definition
| each atom is atracted to the other until a certain point where their electron clouds begin to repell. |
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Term
| how do hydrogen bonds work? |
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Definition
| Hydrogens bound to an electronegative atom have a partial postive charge and are atracted to a second electronegative atom |
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Term
| how do electrostatic interactions work? |
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Definition
| theyre formed between oppositely charged polar groups. THe more polar the atoms, the stronger the bond |
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Term
| of the 4 factors that affect protien folding, rank the strongest to the weakest |
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Definition
1) hydrophobic
2) electrostatic
3)hydrophobic
4)van der walls |
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Term
| what forms the Alpha helix? |
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Definition
| hydrogen bonding between an AA and the AA 4 residues away |
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Term
| how is the B sheet formed? |
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Definition
| H bonding between R groups |
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Term
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Definition
primary -- sequence
secondary -- h bonding
tertiary -- 3d r group interaction
quaternary -- interactions btween chains |
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Term
| Why does the substitution of a single amino acid totally cause sickle cell? |
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Definition
| charged glutamic acid is subistuted for non charged valine. The valine tires to hide in the "sticky patch" on aonther hgb molecule creating a long fibrous polymer. BAAD |
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