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Terms in this set (70)
Why is proline special? screws up what?
it is special because its side chain and A-amino N are involved in a 5 membered ring. thus it has a secondary instead of primary amino group. can interrupt a helixes in globular proteins and forms collagen.
Why is histidine special?
because it is a + amino acid but it is not charged at physiological pH. the pk of its side chain involved N is 6.0.
Your non polar amino acids are also what?
Why is cysteine special?
has a "sulfhydrl" thiol- Sh group... thus can form a di sulfide bond with another cysteine forming-- cystine.. When oxidized... many enzymes active sites need these sulfhydrl groups.
Glycine unique why?
only a-chiral amino acid. thus not optically active so no D or L
All amino acids in proteins are D or L?
What does PKa stand for?
pH at which one half of the protons have been removed. 1/2 pronated
so at Pk1 what amount of Pk1 is in solution what amount of Pk2? what about at pk3?
50-50 pk1 to pk2 50-50 pk2 to pk3
All non polar aka hydrophobic AA's pk1 approx? pk2?
pk1 at 2.3 aka will lose the H off of COOH at that point at pk2 ~ 9.6 will lose a H off of the NH3 attached to the a- carbon.
What is the isoelectric point?
pH at which the overall charge in solution for the AA is 0...
In the body does Co2 act as an acid or a base? whats its antagonist?
acts as an ACID! Bicarb- acts as a base
find the stuff about phosphate
At a ph of 1.5 would something with a pk of 3.5 be mainly protonated or deprotonated?
protonated! thus if was cooh not charged.. but some others might could be.. so protonation doesn't really tell charge all the time.
at physiological ph is the a- carboxyl group protonated or not? what about the a- amino group?
carboxyl will be de- protonated amino protonated
so at a ph of < 2 what will alanines likely charge be? at 6.0 pH? at 10.o pH?
+1 , at 6 pH= 0 at 10.0 = -1 recall start at 0 pH and work your way up each time you pass a Pk you lose a Hydrogen and thus get +1
why is serine special?
has a side group that can be phosphorylated.
Primary structure is what?
sequence of amino acids or sequence of atoms.
what type of bond joins AA's in proteins?
Peptide. the a- carboxyl of one links to the a- amino of the other!
Why are peptide bonds so good?
They resist being broken or denatured takes heat and acid or base long time exposure to break
What is the N terminus? in a peptide bond..
It is the end that has the free or unsubstitued bound NH.. you start your naming there. would at -ly to all 3 letter abrevs in the line except for the last or C terminus which would get full name.
The free C00- should be on the right. gets full name in naming.
are peptide bonds rigid or can they have rotation? where does a peptide <30aa's or a protein gets its rotation?
peptide bonds are like double bonds no rotation get rotation from the a- carbons
protein folding bonds where? what drives the formation of the secondary structure? called?
in the peptide back bone. Secondary structure driven by the hydrophobic effect. Motifs
what is secondary structure?
The regular arrangement of the amino acids near each other in primary structure. a helix b sheet etc... arrangement not order
tertiary structure is what? also called?
is the 3d shape of the folded chain. called domain
arrangement of polypetide sub units in the structure.
all levels of structure contribute to what? which determines?
the native conformation.--- which determines biological function
is the native conformation the highest or lowest energy structure? stable or unstable?
lowest energy, makes it very stable.
what do all proteins backbones consist of ?
Peptide bonds in proteins are trans or cis? means?
they are trans.. not charged but polar.... means the R groups alternate sides of the chain they are on aka R1 superior R2 inferior.
what also determines the native conformation? hint peptide bonds are? planar or can rotate?
Since peptide bonds are PLANAR and thus no movement the rotation of the peptide is do to the rotation around the alpha- carbon
What do glycans attach to most often? AA wise.
Aspargine-- ASN- N --quiz
What stabilizes an alpha helix?
H bonding between backbone N and O that are parrellel to the length and are 4 aa's apart counting them aka n1 with 04
alpha helix what kind of structure? number of aa's per a turn? where are the R groups located?
2nd, 3.6 per turn. they stick out on the sides..
what does proline do to a alpha helix?
inserts a kink! do to secondary amino grp
what do the 5 charged AA do to a alpha helix?
they disrupt it by either forming ionic bonds or by repelling each other.
why does tryptophan screw up an alpha helix if in large numbers?
screws up because it has a bulky side group a double ring
how do isoleucine or valine screw up alpha helixes if in large numbers?
they branch at the beta carbon! valine is a v. shape both are no polar thus hydrophobic just a random fact.
B sheets are made up of what? held together how?
made up of B strands held together by H bonds all the parts of the peptide bonds are involved in H bonding to another strand. aka the =O - N on adjacent strands
In b sheets how are the R groups oriented?
opposite to their neighbor one faces up on the sheet one faces down.
B turns consisit of 4 or more amino acid groupings what two amino acids common here?
Glycine and Proline. and often charged structures.. may have to id one on the test. recall glycine is the smallest r group and proline is the 2ndary amino with a ring.
In B sheet the h bonds are parallel or perpindicular to the sheet? are the strands highly condensed or extended?
Sheets are perpindicular to H bonds. the strands are highly extended.
b sheets parallel means? anti parallel means?
parallel means N- term N-term of two strands on same end anti parrellel means its N term C term on same end
coiled- coiled structure typically mediates what kind of interaction?
mediates protein- protein.
EF hand/helix loop helix mediates?
2ndary structures have what kind of sequence?
Consensus because sequence ultimately determines function.
Zinc finger motif associated with what?
DNA or RNA binding.....think to get a finger you need DNA or RNA.
two amphipathic helices can associate how?
by hydrophobic interactions aka there hydrophobic regions join and there hydrophilic surround..... a alpha helix dimer.
Quiz- what would you expect too see in a Alpha helical structure? Leucine... why?
answer is because it is not charged or an interfering one.... So would form a stable structure.
Quiz- asked which was a secondary structure... was all . But a lot put random coil... as not being one but it is still a secondary structure.
Tertiary structure also known as?
native structure or active structure.
tertiary structure mostly stabilized by what kind of bond covalent or non covalent between secondary structures and what?
non covalent and between secondary structures and things within that can't be classified as being second structure.
name the 3 type of STABILIZING H bonds in tert structure?
H- bonding between peptide groups.
H bond between peptide and side chain group
H bond between 2 side chain groups
Name the other 3 types of stabilizing bonds not Hydrogen. frequent on test...
Ionic bonds N---- O - CR=O
example of all alpha protein?
triose phosphate isomerase TIM is an example of all alpha or alpha beta protein? is TIM a alpha beta twist or alpha beta barrel? What is the sequence used repeated how many times? forms how? What is in the center?
alpha beta barrel.
B-A-B-A repeated 4 or more times
B twist and then the alphas lay down forming outside of barrel
a Hydrophobic b sheet surrounded by amphipathic a helixes
In a protein, a particular arrangement of amino acids or secondary structure that can be found in other proteins can be called a?
If that particular arrangement is related to some function (binding, catalytic, etc.) then it is a?
called a motif. if relates to function then called a domain.
blank -structure refers to the number of subunits, their relative positions, and contacts between the individual monomers in a multimeric protein.
Functional redundancy of amino acids means?
means that a lot of the amino acids within there sub group act the exact same.. meaning that as long as you have the same number of subunits in same order from same groups the protein will fold the same most of the time!!!! ex was globular proteins from animals and plants
what is leukocytosis?
increase in white blood cell count
what is a reticuloycte?
immature red blood cell.
hemoglobin in adults the 4 chains are what? also has a ferrous iron atom Fe+2.... in fetus?
2 alpha 2 beta in fetus 2 alpha 2 gamma
4 types of screwed up hemoglobin? 1. altered exterior?
2. Altered active site? causes?
1. HBs - most harmful type- sickle cell
2. 02 can't bind because 2 of the ferrrous Fe+2 are perm stuck as ferric Fe3+ causes cyanosis- bluing..
3. Altered tertiary structure? what happened?
4. altered quartenary structure? caused by? ex?
3. altered folding pattern GLYCINE has been replaced at B and E sites with ARGININE
4. subunit interface error or from defect synthesis of the alpha or beta chains thalassemia-A no A-chains made.
in sickle cell Beta sub unit of what is changed for what? what does this do? effects shape but also make more or less soluble?
glutamate for valine. creates a hydrophobic region that then binds to other hydrophobic regions creating long fibers in the RBC distorts shape. Since they all clump together also make less soluble. occlude capillaries and thus create microfarcts or dead areas of tissue do to blood loss. creates pain.
folding agents known as chaperones. Chaperones assist in what 2 things?
1) folding of nascent polypeptides made by translation, and 2) re-folding of proteins denatured by environmental damage, such as heat shock.
Molecular chaperones (Hsp 70) bind to what? use what energy source to cause folding?
bind to unfolded nascent polypeptide chains as they emerge from the ribosome, and prevent aggregation, misfolding, and degradation.
Hsp 10 and Hsp 60 are what? do what? also called?
cap and hollow cylinder use ATP to force unfolded proteins to fold..
Lippincott's Illustrated Review - Provides Nice Summaries of Chapter
Know and understand the questions at the end of the book. They tend to be in quizzes and in the exams.
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