Shared Flashcard Set

Details

Biochem Exam 1
n/a
118
Biochemistry
Undergraduate 4
09/22/2013

Additional Biochemistry Flashcards

 


 

Cards

Term
how do you separate polypeptide chains? (4 methods)
Definition
1. pH extremes
2. 8 M urea
3. 6 M guanidine HCl
4. high salt concentration (ammonium sulfate)
Term
what does performic acid oxidation do?
Definition
cleaves disulfide bridges
Term
what are 2 sulfhydryl-reducing agents? what do they do??
Definition
1. mercaptoethanol
2. dithiothreitol/dithioerythritol
-->treat w/ alkylating agent after (like 3-bromopropylamine)

--cleaves disulfide bridges
Term
what does carboxypeptidase A do?
Definition
cleave any residue except Pro, Arg, or Lys (for C-terminal ID)
Term
what does carboxypeptidase B do?
Definition
cleave residues only at Arg & Lys
Term
What does carboxypeptidase C and Y do?
Definition
cleaves residue anywhere
Term
what does trypsin do?
Definition
cleave on C-side of Lys and Arg
Term
what does Chymotrypsin do?
Definition
cleave on C-side of Phe, Tyr, Trp
Term
What does clostripan do?
Definition
attacks Arg more than Lys (similar to trypsin)
Term
what does staphylococcal protease do?
Definition
cleaves C-side of Glu or Asp
Term
What does cyanogen bromide act on?
Definition
acts on methionine residues only
Term
a-helix: how many residues per turn?
Definition
3.6
Term
a-helix: rise per residue?
Definition
1.5 A = 1.5 nm
Term
a-helix: rise per turn
Definition
3.5 * 1.5 A= 5.4 A = .54 nm
Term
a-helix: true repeat
Definition
27 A = 2.7 nm
Term
a-helix: phi?
Definition
-60
Term
a-helix: psi?
Definition
-45
Term
a-helix: angle circumscribed per helix unit
Definition
delta phi = 100 degrees
Term
a-helix: backbone loop that is closed by any H bond contains how many atoms?
Definition
13
Term
B-pleated sheet: rise per residue
Definition
.347 nm (antiparallel)
.325 nm (parallel)
Term
B-pleated sheet: rise per turn
Definition
2 * 3.5 A = 7 A = .7 nm
Term
B-pleated sheet: phi
Definition
~180
Term
B-pleated sheet: psi
Definition
~180
Term
B-pleated sheet: angle circumscribed per helix unit
Definition
delta phi = 180
Term
B-turn contains how many residues?
Definition
4
Term
how does a B-turn work?
Definition
carbonyl C of one residue is H bonded to amide proton of residue 3 residues away
Term
proline is preferred in what position for what types of B-turns?
Definition
proline fits best at position 3 in type I turns, best at position 2 in type II turns
Term
VDW:
-strength range?
-distance range?
Definition
.4 - 4 kJ/mol
.3-.6 nm
Term
H-bond:
-strength range?
-distance?
Definition
12-30 kJ/mol
.3 nm
Term
Ionic interactions:
-strength
-distance
Definition
20 kJ/mol
.25 nm
Term
hydrophobic interactions
Definition
<.4
Term
looking at the table 1.5 life times- what can you conclude as time increases?
Definition
as time increases, more stable interactions (covalent bonds) and phenomena involving agents of genetic info (nucleic acids) come into play
Term
what are 3 things a simplest cell must show a degree of?
Definition
1. degree of metabolism & energy production
2. genetic replication based on template molecule that encodes genetic info
3. formation & maintenance of cell boundary
Term
why do hydrophobic substances tend to coalesce?
Definition
more H-bonded interactions between H2O molecules are possible when they coalesce=entropy driven
Term
what is the formula for dG standard?
Definition
dG standard = -RTln(Keq)
=-2.3*RT*log(Keq)
Term
what does dG standard ' specify?
Definition
dG' specifices that reactants & products are in the ionized form prevailing at pH 7
Term
what is a group transfer potential defined as?
Definition
the free energy change that occurs upon hydrolysis (transfer of a group to water)
Term
what are the 3 reasons for large negative dG' in group transfer potentials?
Definition
1. electrostatic repulsion
2. competing resonance
3. entropy
Term
what is the dG' hydrolysis of ATP?
Definition
-30.5 kJ/mol
Term
what is the dG' of the hydrolysis of PEP (an enol phosphate) & tautomerization?
Definition
-62.2 kJ/mol
Term
what does an enol phosphate after hydrolysis tautomerize to?
Definition
enol-->keto
Term
what is the dG' of creatine phosphate?
Definition
-43.3 kJ/mol
Term
what is the main reason why hydrolysis of creatine phosphate so favorable?
Definition
has an unstable resonance form- where the 2 oxygens attached to the phosphate and interacting w/ each other and with the NH2+ group of creatine
Term
what is the dG' for hydrolysis of acetyl CoA?
Definition
-31.5
Term
why is the hydrolysis of acetyl CoA favorable?
Definition
thio-ester resonance stabilization is less favorable than oxy-ester
Term
what are the nonpolar amino acids?
Definition
V A L I M P F W
Term
proline is technically not an amino acid but a
Definition
alpha-imino acid
Term
tryptophan has what type of R group?
Definition
indole ring
Term
polar, uncharged amino acids?
Definition
Asn/N, Gln/Q, Tyr/Y, Thr/T, Ser/S, Cys/C, Gly/G
(Guards, Stop The Next Queen, You C*nt)
Term
which group of amino acids can form hydrogen bonds with water?
Definition
polar, uncharged amino acids (except glycine)
Term
which amino acids have a net negative charge at neutral pH?
Definition
aspartic acid & glutamic acid (the acidic amino acids)
Term
which amino acids have a positive net charge at neutral pH?
Definition
histidine, arginine, and lysine
Term
histidine contains what type of R group?
Definition
imidazole
Term
arginine contains what type of R group?
Definition
guanidino
Term
which amino acids are hydrophobic?
Definition
A, G, L, I, F, P, V
(All Good Ladies, If Fucked, Put Viagra)
Term
which amino acids are hydrophilic?
Definition
R, N, D, C, E, Q, S, T
Term
which amino acids are amphipathic?
Definition
K, M, W, Y
(Kill Mary in WY (Wyoming))
Term
what 3 amino acids absorb UV light?
Definition
Phe, Tyr, Trp
Term
which amino acid is destroyed by acid hydrolysis?
Definition
tryptophan
Term
which 2 amino acids convert to 2 other amino acids? what gets released in the process?
Definition
Asparagine & Glutamine are converted to Aspartic acid & glutamic acid; the amide-N released as NH4+
Term
peptide bond between what type of amino acids are resistant to acid hydrolysis?
Definition
peptide bonds between hydrophobic amino acids
Term
what role does the amino acid sequence play in protein structure?
Definition
all the information necessary for folding the chain into its native structure is contained in the primary structure of the polypeptide
Term
the angle about the Ca-N bond is denoted as?
Definition
phi (o w/ line through it)
Term
angle about the Ca-C bond is denoted as?
Definition
psi (triton looking symbol)
Term
left handed helices tend to have positive/negative values of phi/psi?
Definition
phi and psi values are both positive
Term
right handed helices tend to have positive/negative values of phi/psi?
Definition
phi and psi values are both negative
Term
right handed alpha helices are made with only D/L amino acids?
Definition
D amino acids
Term
right handed alpha helices are CCW/CW?
Definition
CW
Term
left handed alpha helices are CCW/CW?
Definition
CCW
Term
secondary structures form when what 2 constraints are met?
Definition
1. sterically permissible phi & psi values
2. stablization through H-bond formation
Term
what amino acids tend to be helix formers?
Definition
A, E, F, H, I, L, M, Q, R, W, Y
Term
what amino acids tend to be helix breakers?
Definition
proline
Term
proteins fold to form the most stable structures. stability arises from: (2)
Definition
1. formation of large # of intramolecular H bonds
2. reduction in solvent accessible surface area of the proetin when it folds
Term
a-Keratin has what type of secondary structure?
Definition
311-314 residue-long alpha helical rod secments capped w/ non helical N & C termini
Term
a-Keratin's primary structure of the helical rod consists of what type of repeats?
Definition
7 residue repeats, where first and 4th positions are nonpolar
Term
what is the usual sequence for fibroin & B-keratin?
Definition
Gly-Ala/Ser-Gly-Ala/Ser-Gly...
Term
what is unique about the structure of B-keratin?
Definition
residues of B-sheet extend alternatively above & blow the place-->placing all glycines on one side & all alanines and/or serines on the other side
Term
what is the basic unit of collagen?
Definition
tropocollagen
Term
what is unique about tropocollagen and why does it happen?
Definition
unusual amino acid composition of collagen creates 3 intertwined helical strands, the amino acid composition that includes lots of prolines and hydroxyprolines
Term
what is the rise per residue of tropocollagen?
Definition
2.9 A=.29 nm
Term
what is the # of residues per turn of tropocollagen?
Definition
3.3
Term
what does the amino acid sequence of tropocollagen usually contain?
Definition
long stretches of Gly-Pro-Pro/HyP
Term
every 3rd residue of tropocollagen is what? why?
Definition
every 3rd residue of each chain faces the crowded center of the helix- only glycine fits here
Term
what bonds stabilize the helix?
Definition
interchain H bonds involving HyP
Term
why does the protein core consist primary of a-helices & b-sheets?
Definition
highly polar NH & C=O moieties of peptide backbone must be neutralized in hydrophobic core==>extensive H bonded nature of the 2 structures is ideal for this purpose
Term
the peptide chain of globular proteins, to adopt the most stable 3' structure must do what 2 things
Definition
1. satisfy constraints inherent in structure building
2. fold to bury hydrophobic side chains
Term
what are the 2 forces that drive 3' folding
Definition
-peptide chain must fold so as to "bury" the hydrophobic side chains, minimizing their contact w/ water
-peptide chains, composed of L-aino acids, have tendency to undergo a "right handed twist"
Term
what is the large contribution to the thermodynamic driving force for folding of proteins?
Definition
the largest favorable contribution to folding is the entropy term for the interaction of nonpolar residues w/ the solvent
Term
intrinsically unstructured proteins are usually composed of what amino acids?
Definition
abundance of polar residues & lack of hydrophobic residues
Term
What are the 4 advantages of 4' association?
Definition
1. stability: surface to volume ratio becomes smaller
2. genetic economy & efficiency: less DNA is needed to encode monomer that assembles into a multimer vs. DNA needed to encode one large polypeptide
3. bringing catalytic sites togehter
4. cooperativity: binding of ligand to one subunit alters the likelihood of binding ligand at other subunits
Term
sugars with an amino group at C2 are what types of sugars?
Definition
amino sugars
Term
what is starch?
Definition
plant storage polysaccharide
Term
what are the 2 forms of starch?
Definition
amylose & amylopectin
Term
amylopectin branches per how many residues?
Definition
branches in amylopection occur every 12-30 residues
Term
what type of bond does amylose have?
Definition
a(1,4) linkage
Term
what type of linkage do amylopectin branches have?
Definition
a(1,6) linkage
Term
what can glucoamylase cleave?
Definition
a(1-->4) and a(1-->6) glycosidic bonds=break oligosaccharides down to free glucose
Term
what are the structural differences between amylose and cellulose?
Definition
amylose are a-1,4-linked D glucose units vs. cellulose that has B-1,4-linked D glucose units
Term
what makes cellulose so strong?
Definition
the H bonds between the sheets strengthen the structure (interchain H bonds)
Term
what are glycosaminoglycans?
Definition
linear chains of repeating disaccharied in which one unit is an amino sugar and one/both are negatively charged
Term
glycoasminoglycans are components to what?
Definition
proteoglycans
Term
N-linked saccharides are attached via what?
Definition
via amide nitrogens of asparagine residues
Term
O linked saccharides are attached via what?
Definition
attached to hydroxyl groups of serine, threonine, or hydroxylysine
Term
what is the structure of peptidoglycan?
Definition
tetrapeptides link adjacent backbone chains
-notice the isogluatmate linkage in the tetrapeptide chain
-here is wehre there is an unusual gamma-carboxyl linkage (rather than at the alpha carbon)
Term
Proteoglycans are?
Definition
glycoproteins whos carbohydrates are mostly glycosaminoglycans
Term
what are fatty acids comprised of?
Definition
alkyl chains terminated by caroxylic acid groups
Term
what is the X:Y symbol for palmitic & stearic acid?
Definition
C16:0
C18:0
Term
what is the X:Y symbol for oleic and linoleic acid? where are the double bonds
Definition
C18:1, 9
C18:2, 9 & 12
Term
what is the X:Y symbol for linolenic & arachidonic acid?
Definition
C18:3, 9, 12, 15
C20:4, 5, 8, 11, 14
Term
lactose linkage?
Definition
gal-B-1,4-glu
Term
maltose linkage?
Definition
glu-a-1,4-glu
Term
isomaltose linkage?
Definition
glu-a-1,6-glu
Term
cellobiose linkage?
Definition
glu-B-1,4-glu
Term
sucrose?
Definition
glu-1a-B2-fru
Term
globular or fibrous proteins are soluble in aqueous solutions?
Definition
globular- fibrous proteins tend to be structural proteins that are insoluble
Term
how do membrane proteins fold?
Definition
fold so that hydrophobic amino acid side chains are exposed in membrane associated regions
Term
secondary structures are a result of what?
Definition
result of H bonding
Term
what are the forces driving quaternary association?
Definition
-dimerization=gives you energy
-loss in degrees of freedom upon that dimerization=loss of energy
[-favorable VDW interactions offset by VDW lost due to removal of solvent]
BUT-- favorable hydrophobic interactions you energy AND so does making the surface area smaller

=all together net free energy of -50 kJ
Supporting users have an ad free experience!