Topics List E1 Flashcards
polarity
results from uneven partial charge distribution btw various atoms in a compound.
e-‘s in these bonds are unequally shared btw the bond of a partially positive and partially negative atom.
nonpolar
when molecules have atoms w/ = or nearly = electronegativities (small dipole moment)
or
it has polar bonds but molecular geometry is symmetrical. (dipoles cancel e/o out)
Bronsted-Lowry Acids
H+ donors
Bronsted-Lowry Bases
H+ acceptors
H-bonds are a ____ force compared to a covalent bond.
weak
H-bonding forms?
the basis of a double-helix in vivo.
In the peptide backbone of AA’s the H donors are the?
the H atoms attached to the O of the carbonyl or the H attached to the N of the amine group.
In the peptide backbone of AA’s the H acceptors are the?
the more e-neg atoms, the O of the carboxyl group or the N of the amino group.
What is the first law of thermodynamics?
E is conserved, it cannot be created / destroyed, only converted from one form to another.
What is Gibbs Free E?
a thermodynamic quantity = to the enthalpy (of a system / process) minus the product of entropy and the absolute temp.
If dG is (+) then the rxn is?
nonspontaneous, an input of external E necessary for rxn to occur.
If dG is (-) then the rxn is?
spontaneous, occurs w/o external E input.
activation E
the min amount of E req’d to activate atoms / molecules to condition in which they can undergo a rxn.
These can decrease the activation E req’d for a rxn to occur.
enzymes
What is a spontaneous rxn?
rxn that favors products at conditions under which rxn is occurring.
equilibrium
chemical state when forward rate = reverse rate.
Equilibrium is related to free E by?
Keq; equilibrium constant.
If there’s no change in the reactants or products there’s no change in?
dG.
Keq
equilibrium constant, defines relative conc’s of products and substrates.
If you ↑ [S] you ___ Keq?
decrease
If you ↑ [P] you ___ Keq?
increase
If there’s more reactants (substrates) the Keq is ___ and the denominator is ___?
Keq - smaller
denominator - larger
If there’s more product the Keq is ___ and the numerator is?
Keq - larger
numerator - larger
For Gibbs free E if the denominator is ___ then ___ E is needed.
denominator larger
less E needed
If there are less ___ it is ___ to move the rxn forward.
less products
easier to move rxn forward
A(n) ___ does not change the Free E (dG)
enzyme.
rxn rate
A + B → C
If the rxn rate is A + B → C and A is halved, the rate of the rxn will be?
halved.
Rxn rate depends on?
[products] and [reactants]
pKa measures?
acid strength.
Ka
acid ionization constant
How do you find the pKa?
-logKa
If the pKa is high it is less ___ and the proton dissociates ___ easily.
less acidic
proton dissociates less easily
If the pKa is low it is less ___ ?
less basic
If the pH is low it’s more ___ and more likely to be ___.
pH low
more (+)
more likely to be protonated
If the pH is high it’s more ___ and more likely to be ___.
pH high
more (-)
more likely to be deprotonated.
How do you calculate pH?
-log[H+]
buffer
chemical systems resistant to changes pH; help maintain neutral pH.
Henderson-Hasselbalch Eqn
calculates the pH of a buffer system.
pH = pKa +log [A-]/[HA]
peptide bond
linkage btw 2 AA’s:
amide linkage btw carboxyl of AA and amino group of next AA. (recurring)
linear polymers of AA’s.
When a peptide bond is formed a(n) ___ is removed to form a(n) ___ bond; therefore it is and example of ___.
water molecule
amide
dehydration
A peptide bond is a(n) ___ linkage of ___ configuration.
covalent
trans
primary structure
seq of AA’s that make up a polypeptide chain.
The primary structure of a protein (it’s AA sew) is important because it?
drives folding and intermolecular bonding of the linear amino chain which ultimately determines the proteins unique 3D shape.
alpha helices
coiled structure of many proteins, consists of single chain of AA’s stabilized by H-bonds.
An alpha helix is a ___ structure.
secondary
A beta helix is a ___ structure?
secondary
beta sheets
parallel or antiparallel, form pleated sheets, R groups play a role.
What is a parallel beta sheet?
C-terminus and N-terminus on same sides.
What is an antiparallel beta sheet?
C-terminus and N-terminus on each side.
What are some other structural components of secondary structures?
coiled coil, zinc finger, hairpin loops.
What are the 2 ends of a primary structure?
- Amino / N-terminus
2. Carboxy / C-terminus
motifs
combinations of secondary structures, determined by appearance not function.
domains
portion of protein that retains structure / function in absence of rest of protein, discretely folding 3D structure.
helix-turn-helix is an example of a?
motif
DNA-binding domain is an example of a?
domain
Which way do we read primary structures?
Amino / N-terminus to Carboxy / C-terminus.
The ___ structure is held together by H bonding.
secondary
tertiary structure
gives overall 3-D shape of protein, combines elements of secondary structure, beta sheet and alpha helix.
What are the stabilizing forces involved in protein structure?
van der Waals forces, H-bonds, disulfide bridges, salt bridges.
monomers
single chains of AA’s folded into active protein.
___ can be subunits of multimers
monomers
multimers
several subunits, each has its own protein monomer (polypeptide chain), each labeled based on function (catalytic, regulatory, etc.), not covalently linked.
Dimers, trimers, and tetramers are examples of?
multimers
Somatic hypermutation (SHM)
occurs in differentiation B cells and enables even more variety in the Fab domains of Ab’s.
ACE-binding residues
AA mutations
“Sustainer” patients
↑ anti-SARS-CoV19 immunity over successive draws.
“Decayer” patients
↓ immunity along w/ ↓ Igs
What can modify / change an AA?
Change in pH, phosphorylation, disulfide bond, and a mutation of the genome
disulfide bonds
play key role in stabilizing protein structures, disruption strongly associated w/ loss of protein function and activity
Enzyme: hexokinase
1st enzyme that functions in glycolysis
Enzyme: phosphatase
removes a phosphate
Enzyme: lactase
breaks down lactose
Enzyme: sucrase
breaks down glucose
-ase
enzyme
Enzymes stabilize the ___ by donating e-‘s that the enzyme will eventually recover.
transition state
Enzymes are also called?
catalysts
Enzyme: chymotrypsin
digestive enzyme
Enzyme: protease
degrades proteins
Enzyme: ACE2
human enzyme, helps virus infect us
Enzymes increase ___ , decrease ___, and don’t effect ___.
increase rate of rxn
decrease activation E,
don’t effect dG.
fusion protein
protein made from fusion gene, created by joining parts of 2 diff genes.
At least 2 domains.
Functions of fusion proteins?
- aids in cloned gene purification
- report expression level
- histochemical tags to visualize location of proteins.
epitope tags
biological structure / seq (protein / carbohydrate) that acts as an antigen which is recognized by an antibody.
Functions of epitope tagging?
- detect proteins when no Ab is available.
- characterize newly discovered proteins / low abundant proteins.
- can id / purify favorite protein
Protein Purification: Salting Out
a lot of salt makes charged molecules precipitate
What are the Column-based methods of protein purification?
- Size-exclusion chromatography
- ion-exchange chromatography
- affinity chromatography
Protein Purification: Size-Exclusion Chromatography
separates proteins based on size.
In Size-Exclusion Chromatography the ___ proteins reside longer in beads and the ___ proteins elute in early fractions.
small reside longer.
large elute early
The gel beads in Size-Exclusion Chromatography have pores that?
allow smaller molecules to enter and excludes molecules larger than the pores.
Protein Purification: Ion Exchange Chromatography
separates proteins based on charge.
In Ion-Exchange Chromatography the stationary phase is?
charged, binds proteins w/ opp charge.
In Ion-Exchange Chromatography you can elute using?
salt, pH change.
Protein Purification: Affinity Chromatography
isolates specific proteins by taking advantage of specific interactions btw protein and stationary phase.
The stationary phase of Affinity Chromatography can be loaded with?
ligand / Ab / epitope tags
Protein Purification: Immunoprecipitation
uses Ab’s, Ig Fc linked beads which work like stationary phase in a column.
Ab’s heavy, separate using centrifuge.
Which of the following won’t affect your antibody’s binding to a target protein? A. Change in the epitope B. Change in the pH C. Change in the Fab D. Change in the Fc E. All of the above will affect your antibody’s affinity for the target it usually recognizes.
D. Change in the Fc
All chromatography techniques involve movement of a compound with a ___ over a ___?
mobile phase over a stationary phase.
Yield is equivalent to?
total amount protein (activity) in final sample / amount protein (activity) in crude sample
Fold Purification equivalent to?
specific activity in final sample / specific activity in crude lysate
Suicide Inhibitors
directly poison enzyme
covalently modify enzyme active site, irreversible block function.
A pesticide is an example of a?
suicide inhibitor
The only type of irreversible inhibitor is?
suicide inhibitors
What are the 3 types of reversible inhibitors?
Competitive
Uncompetitive
Noncompetitive
Competitive Inhibition
recognizes molecules similar to shape of substrate that binds to active site.
competes w/ substrate
can overcome by increasing substrate.
Competitive Inhibitors increase ___ but do not change the ___.
increase Km
don’t change Vmax
Competitive inhibitors will do what on a double reciprocal graph?
intersect with the line where no inhibitor is present.
Uncompetitive inhibitors will do what on a double reciprocal graph?
will not intersect with the line where no inhibitor is present.
Uncompetitive Inhibitors decrease both ___ and ___.
Km and Vmax
Uncompetitive inhibitors bind the ___.
{ES] complex
Uncompetitive requires ____?
substrate.
Noncompetitive Inhibition has no change in ___ but decreases ___.
no change in Km
decreases Vmax
Increasing [S] doesn’t alleviate inhibition.
In Noncompetitive Inhibition the ___ and ___ bind at different sites
substrate and inhibitor
Noncompetitive Inhibition will do what on a double reciprocal graph?
only intersect on the x-axis, at the very beginning of the line on the (-) side of the y-axis.
Protein: aquaporin
transmembrane protein.
Acts as pore / channel in membrane, extends above / below plasma membrane.
Selectively allows water passage in / out of cell.
Aquaporin has a(n) ___ interior and a(n) ___ exterior
hydrophilic interior
hydrophobic exterior
Water diffusion in aquaporin is controlled via?
- Gating: controlled by phosphorylation / ionization of R groups.
- Trafficking: response to environmental osmolarity changes (rain)
Protein: chymotypsin
Digestive enzyme
Cleaves dietary proteins into peptides
Contains active site and regulatory site.
The composition of chymotrypsin is?
2 beta barrels
1 short alpha helix.
Structure of chymotrypsin
Protease: enzyme that degrades proteins.
3 polypeptides linked by S-S.
Starts as inactive precursor, trypsin then cleaves off inhibitory domain to activate it.
Protein: Collagen
structural protein
Fibrous protein, concentrated in muscle, connective tissue.
Composition of Collagen
Composed of triple helix:
Glycine (33%)
Proline (16%)
Hydroxyproline (16%)
Protein: Antibodies / Immunoglobulins (Ig)
binding proteins
Large proteins made by immune system that recognize, bind to antigens.
Function of Antibodies / Immunoglobulins (Ig)
Detect foreign bacteria / viruses.
Mark for engulfment by phagocytic cells (destruction).
Structure of Antibodies / Immunoglobulins (Ig)
Y
Solid-Phase Peptide Synthesis (SPPS)
best for small peptides doesn’t include protein chaperones
modifying enzymes
cellular cond’s hard to replicate in test tube system.
Why use protein overexpression instead of SPPS?
larger size range, benefits of other cell components.
lysosome
membrane-bound organelle, contains digestive enzymes, break down excess / worn-out cell parts.
Protein: Src
non-receptor tyrosine kinase encoded by SRC gene.
transduces signals involved in control of cellular processes (proliferation, differentiation, motility / adhesion)
carbonic anhydrase
in RBC
Aids in conversion of CO2 to carbonic acid and bicarbonate ions.
Converts bicarbonate ions back to CO2 (breathe out).
ATCase
catalyzes committed step in pathway that ultimately yields pyrimidine nucleotides such as cytidine triphosphate (CTP).
spike protein
glycoprotein
allows coronaviruses to enter cells
