Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
73 Cards in this Set
- Front
- Back
|
What are amino acids (in terms of functional groups)?
|
-an amino derivative of carboxylic acids (both are linked to the alpha carbon)
|
|
|
What are Zeitterions?
|
-at physiological pH, the amino group os protonated and the carboxyl is ionized
|
|
|
What are the ploar uncharge amino acids?
|
-glycine
-serine -asparagine -threonine -cysteine -glutamine -tyrosine |
|
|
What are thh hydrophobic amino acids?
|
-leucine
-proline -alanine -valine -methionine -tryptophan -phenylalanine -isoleucine |
|
|
What are the basic amino acids?
|
-lysine
-histidine -arginine |
|
|
What are the acidic amino acids?
|
-aspartic acid
-glutamic acid |
|
|
How many of the 20 AA are chiral?
|
-19 out of 20!
(exist as stereoisomers) |
|
|
What are stereoisomers?
|
-they have same molecular formula but different arrangements in space
|
|
|
There are about 200 naturally occurring AA. How can there be so many?
|
-exist as L-AA's in biochemical pathways
-D-AA's in microbe cell walls and antibiotics -Post-translationally modified AA |
|
|
What is the primary sequence of proteins?
|
-all peptide bonds are the same
-only sequence of side chains is different -vary widely in size and complexity |
|
|
Do cells contain lots of protein?
|
Yes, Rat liver has a lot. E-coli is a close second. Even spinach has protein!
|
|
|
What are the essential amino acids?
|
-arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tyrptophan, valine
|
|
|
What are the nonessential amino acids?
|
-alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine
|
|
|
Which two essential amino acids are actually only needed in juveniles of rats and humans?
|
-arginine
-histidine |
|
|
How does a Ramachandran plot work?
|
-only white spots are possible bond angles.
|
|
|
What is amino acid analysis?
|
-finding what amino acids are present and in what amounts in a protein
|
|
|
What is the sequence of amino acids (not analysis)
|
-finding the unique sequence of amino acids in a protein
|
|
|
How do you perform acid hydrolysis of peptides?
|
1) make up in 6 N HCL
2) heat at 110 C for 24 hours |
|
|
What are different ways of separating out amino acids?
|
-peptide hydrolysis
-chromatography -chromatogram -the Ninhydrin reaction |
|
|
Is the peptide bond flat or bent? Why?
|
-bond lies flat due to double bond character (DBC).
*Double bond moves between N=C and C=O |
|
|
For the 20 amino acids we learned, what conformation are they even though they're not drawn that way?
|
-'L' acids
|
|
|
What are two amino acids that are rarely found in proteins?
|
-tryptophan
-thyamine |
|
|
Which amino acid usually has disulfide bonds?
|
-cystein
|
|
|
what two groups will be destroyed if they are put in an acid hydrolysis?
|
-glutamine
-asparage (amide groups get hydrolized) *tryptophan can't stand it either |
|
|
What is the point of Ninhydrin in a chromatogram?
|
everything turns purple except proline which is yellow
|
|
|
What does the height indicate of the peaks in a chromatogram?
|
-amount of amino acid present
|
|
|
What are 4 chromatographic methods?
|
1) adsorption
2) ion exchange 3) partition 4) gel permeation |
|
|
How does ion exchange work?
|
-AA's interact with a stationary charge
|
|
|
How does partition work?
|
-use of a liquid that separates objects
|
|
|
What does gel permeation do?
|
-acts as a molecular sieve by separating large sizes first
|
|
|
What is the problem with gel permeation?
|
-it's hard to find a medium that won't cause adsoption or ion exchange
|
|
|
Once again (and then some), what are the problems with acid hydrolysis?
|
-tryptophan destroyed
-glutamine and asparagine hydrolysed -serine and thronine lowered (desaturation) |
|
|
Why do scientists still use this method?
|
-testing facilities insist on it!
|
|
|
How is the procedure for Ion exchange chromatography?
|
1)add cation exchange bead before sample
2) add mixture of Asp, Ser, Lys 3) add Na+ (such as NaCl): Asp lets go first due to least positive charge 4) increase Na+: Ser elutes next 5) increase Na+ more: Lys will elute last since it has highest charge |
|
|
What protein is sometimes able to denature and renature?
|
-RNAase
|
|
|
What are two major protein sequencing reagents?
|
-Sangers Reagent (DNFB)
-Dansylchloride |
|
|
What are 4 major protein cleaving reagents?
|
-Chymotrypsin
-Trypsin -Endoprotease V8 -Cyanogenbromide |
|
|
Where do cleaving reagents cleave?
|
-on carboxy side of group
|
|
|
How does Chymotrypsin work?
|
-cleaves on carboxy side of: Phe, Tyr, and Trp
-works on the aromatics |
|
|
How does Trypsin work?
|
-cleaves on carboxy side of: Lys and Arg.
-works on basic groups |
|
|
How does Endoprotease V8 work?
|
-cleaves on carboxy side of: Glu or Asp
-works on strong acidic groups |
|
|
How does Cyanogenbromide work?
What is different with this reagant from the others? |
Converts Met into homoserine
*Cyanogenbromide is a chemical reagant NOT an enzyme, nor does it cleave. |
|
|
What is the major difference between a twisted fiber and a pleated fiber?
|
-twisted can stretch to twice the length and back again; pleats barely increase before returning to form
|
|
|
Where do the characteristics of fibrous proteins come from?
|
-a result of their sequence and repeated bond angles
|
|
|
What amino acids make up silk fibroin and what is their ratio?
|
-gly, ala, ser
-3:2:1 ex; g-s-g-a-g-a-g-s-g-a-g-a-g-s |
|
|
What shape is silk fibroin?
|
-found in beta pleated sheets
|
|
|
How does silk stretch in terms of wool?
|
-very poorly
-doesn't bounce back |
|
|
What makes up alpha keratins?
|
-alpha helices (this is how you would make string into a rope)
|
|
|
What component of wool makes it so stretchy?
|
-sulfur content: it has cystein which has disulfide bonds
|
|
|
Is wool an alpha keratin?
|
Yes
|
|
|
What item makes up 25-50% of the protein in vertebrates?
|
-collagen
|
|
|
What are the key characteristics to collagen?
|
-very insoluble
-strongly resists stretching -has lots of gly and pro (or hydroxypro which is more stable) |
|
|
What is the sequence for collagen?
|
-mostly repeating Gly-X-Pro
|
|
|
Why is there so much Gly found in collagen?
|
-it is woven tightly and only Gly can fit in the center where the twists meet
|
|
|
What are the fours levels of protein stucture?
|
-primary
-secondary -tertiary -quartenary |
|
|
How many levels of protein structure does hemoglobin show?
|
-all four levels
|
|
|
Describe the first level of protein structure: primary
|
-primary structure is the order of AA's in the polypeptide
|
|
|
Describe secondary structure.
|
-secondary structure is regularities in local conformations
|
|
|
Describe tertiary structure.
|
-tertiary structure is the completely folded protein, interactions may be between distant parts of the sequence
|
|
|
Describe quarternary structure.
|
Quarternary structure subunit interactions in an oligomeric protein
|
|
|
What causes Sickle-Cell anemia?
|
-An alteration in the sequence of the hemoglobin beta-chain at position 6 from Glu to Val
|
|
|
What affect does the change in hemoglobin have on shape of RBC's?
|
Deoxyhemoglobin is more hydrophobic in one area and this leads to the formation of long rigid fibers
|
|
|
What is denaturation?
|
-disruption of native conformation of a protein, with loss of biological activity
-can be caused by heating or chemicals (very small energy) |
|
|
How can denaturation be monitored?
|
-monitor changes in ultraviolet (blue), viscosity (red), optical rotation (green).
|
|
|
How does 'in vivo' (inside cell) protein folding occur?
|
-folded proteins occupy a very low-energy well which makes it very stable
-proteins fold spontaneously into this conformation -folding continued by previous folds through interactions -folding is extremely rapid <1s - |
|
|
As a protein is folding, what happens to its shape and why?
|
-the polypeptide collapses in upon itself due to the hydrophobic effect
-an intermediate "molten globule" forms with elements fo secondary structure -backbone rearranged to acheive a stable native conformation |
|
|
What is RNase?
|
-Anfinsen denatured it using 8 M urea and beta mercaptoethanol (ME)
-then he removed them to allow refolding (it didn't work) -he added catalytic amounts of beta ME and RNase reformed to 100% of its activity and function! He won the nobel. |
|
|
What does the hydrophobic effect contribute in detail to protein folding?
|
-nonpolar side chains associate causing a polypeptide chain to collapse to the molten globule
-nonpolar chains inside while polar and charged side chains remain on surface facing water |
|
|
What is the driving force for protein folding?
|
-the LARGE increase in entropy from water released to bulk solvent!
*hydrophobic collapse of a polypeptide occurs at the same time as formation of secondary structures |
|
|
How does hydrogen bonding contribute to protein folding?
|
-contributes to cooperativity of folding
-helps stabilize secondary structures and native conformation |
|
|
How do Van der Waals interactions contribute to protein folding?
|
-VDW contacts occur between nonpolar side chains and contribute to stability
-Charge-Charge interactions between oppositely charged side chains in protein interior also may stabalize |
|
|
What is Anfinson's Flicker hypothesis?
|
I don't know!
-prepared antiserum to native Staph Nuclease or to a peptide fragment of aminoacids I-99 |
|
|
How did Anfinson go about his Flicker Hypothesis?
|
-purified antibodies to peptides through affinity chromatography
-Introduced antibodies into native conformation over the peptide column -had same effect on native form as it did from the peptide |
