Structure and function of proteins and their constituent amino acids Flashcards
absolute configuration at the alpha position
All chiral amino acids in eukaryotes are L, and have their amino acid therefor drawn at left in Fischer Projections.
All chiral amino acids are S except cysteine.
All amino acids are chiral but glycine.
The alpha carbon is adjacent to the carbonyl.
Amino acids as dipolar ions
pKa of group is the pH at which, on average, half are protonated and half are not.
Above that pKa, the majority of the species is deprotonated.
pKa1 is the -COOH, pKa2 is the -NH2, pKa3 is the R group.
A whole amino acid is a zwitterion at its pI.
Titration curve is flat at the pKa’s and vertical at the pI.
Like Icharus, amino acids lose protons as they ascend.
Acidic amino acids
Glutamatic acid, Glu, E
Aspartatic acid, Asp, D
Negatively charged at phys pH (7.4)
Basic amino acids
Histidine, H, His
Arginine, R, Arg
Lysine, Lys, K
Positive at physiological pH
Hydrophobic
LIMPVAG (as well as W and F)
Hydrophilic
GSTAC (and Y)
oligopeptides
up to 20
resonance between amino nitrogen and carbonyl provides
rigidity
hydrolysis of amino acids
enzyme adds H to N and OH to C
secondary structure
alpha helix or beta sheet
helix breakers
glycine and proline
turns of beta sheets
glycine and proline
Denaturing
reduced to primary structure.
heat adds energy which overcomes hydrophobic interactions.
solutes can overcome cistine, H-bonds, and other side chain interactions.
Isoelectric point
average the two pKa’s flanking the pI.
No charged side chain, pI around 6.
positive side chain (basic), pI above 6.
Non-enzymatic protein function: binding
ex: hemoglobin, tscription factors, ca-binding.
transport or sequester.
transport affinity varies much with environment.
sequester affinity high across large range of conc.
Non-enzymatic protein function: cell adhesion
integral membrane proteins. surface of most cells. bind ECM and or other cells. three families: cadherins, integrins, selectins.
cadherins
group of glycoproteins. mediate ca-dependent cell adhesion. often hold similar cell types together: E-cadherin for epithelial, etc.
integrins
binding/communicating with ECM. Cellular signalling. Influence cellular function such as division. Ex: platelets use them to stick to fibrinogen, which triggers platelets to stabilize clot.
selectins
unique in that they bind to carbs projecting from other cells. weakest bond of CAMs. white blood cells and endothelial cells lining blood vessel. role in host defense including white blood cell migration and inflammation.
immunoglobulins
made by B-cells. can neutralize antigen(pathogen), mark pathogen for destruction for other WBC right away, or agglutination of antibody and antigen into large insoluble complex that can be phagocytized by macrophages. heavy chains together by disulfide. each light chain with each heavy disulfide.
Non-enzymatic protein function
some structural proteins, such as motile cilia and flagella, and sarcomeres, have motor function in the presence of motor proteins. motor proteins also display enzymatic function, acting as ATPases that power conformation changes necessary for motor function. motor proteins have transient interactions with either actin or microtubules.
myosin
primary motor protein that interacts with actin. thick filament in myofibrils. can be involved in cellular transport.
kinesins and dyneins
assoc with microtubules. vesicle transport. kinesin to positive end, such as to synapse of neuron.
kinesin
aligning xsomes during metaphase. depolymerizing microtubules during anaphase.
dynein
sliding movement of cilia and flagella. toward negative end of MT. Ex: waste and recycled NT toward soma.
function of enzymes in catalyzing biological reactions
lower activation energy. increase reaction rate. do not alter equilibrium constant. not changed or consumed in reaction and so appear in product and reactant side. pH and temp sensitive with optimal activity at specific pH and temp ranges. do not affect overall deltaG. specific for particular reaction or class of reactions.
oxidoreductase
catalyze oxidation-reduction reactions. often have cofactor that acts as electron carrier.
transferase
catalyze movement of functional group from one molecule to another. often called transferases, but also include kinase.
hydrolase
breaking down of compound into two with addition of water. commonly named after substrate. examples are phosphatases, peptidases, nucleases, lipases.
lyase
cleavage of one into two without water. reversible. often called synthetase in reverse.
isomerase
rearrangement of bonds within a molecule. might also be classified as oxidoreductases, transferases, lyases. catalyze reations between constitutional AND stereoisomers
LI’L HOT
ligase, isomerase, lyase, hydrolase, oxidoreductase, transferase
ligase
addition or synthesis generally between large similar molecules. often require ATP. synthesis with smaller molecules generally accomplished by lases. examples of ligase are nucleic acid synthesis and repair.
active site model
no alteration of secondary or tertiary structure necessary upon binding of substrate
induced fit
endergonic binding. exergonic letting go.
cofactors
don’t carry, but participate in reaction. inorganic.
coenzyme
organic. often carrier. NAD+.
prosthetic group
tightly bound coenzyme or cofactor
apoenzyme
does not include cofactor
vitamin
organic cofactors and coenzymes
mineral
inorganic cofactors
charge of DNA
negative
temperature change, effect on enzyme
wrong geometry, misfolding
