Structure and function of proteins and their constituent amino acids

Question 1

absolute configuration at the alpha position

Answer 1

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.

Question 2

Amino acids as dipolar ions

Answer 2

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.

Question 3

Acidic amino acids

Answer 3

Glutamatic acid, Glu, E
Aspartatic acid, Asp, D
Negatively charged at phys pH (7.4)

Question 4

Basic amino acids

Answer 4

Histidine, H, His
Arginine, R, Arg
Lysine, Lys, K
Positive at physiological pH

Question 5

Hydrophobic

Answer 5

LIMPVAG (as well as W and F)

Question 6

Hydrophilic

Answer 6

GSTAC (and Y)

Question 7

oligopeptides

Answer 7

up to 20

Question 8

resonance between amino nitrogen and carbonyl provides

Answer 8

rigidity

Question 9

hydrolysis of amino acids

Answer 9

enzyme adds H to N and OH to C

Question 10

secondary structure

Answer 10

alpha helix or beta sheet

Question 11

helix breakers

Answer 11

glycine and proline

Question 12

turns of beta sheets

Answer 12

glycine and proline

Question 13

Denaturing

Answer 13

reduced to primary structure.
heat adds energy which overcomes hydrophobic interactions.
solutes can overcome cistine, H-bonds, and other side chain interactions.

Question 14

Isoelectric point

Answer 14

average the two pKa’s flanking the pI.
No charged side chain, pI around 6.
positive side chain (basic), pI above 6.

Question 15

Non-enzymatic protein function: binding

Answer 15

ex: hemoglobin, tscription factors, ca-binding.
transport or sequester.
transport affinity varies much with environment.
sequester affinity high across large range of conc.

Question 16

Non-enzymatic protein function: cell adhesion

Answer 16

integral membrane proteins. surface of most cells. bind ECM and or other cells. three families: cadherins, integrins, selectins.

Question 17

cadherins

Answer 17

group of glycoproteins. mediate ca-dependent cell adhesion. often hold similar cell types together: E-cadherin for epithelial, etc.

Question 18

integrins

Answer 18

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.

Question 19

selectins

Answer 19

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.

Question 20

immunoglobulins

Answer 20

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.

Question 21

Non-enzymatic protein function

Answer 21

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.

Question 22

myosin

Answer 22

primary motor protein that interacts with actin. thick filament in myofibrils. can be involved in cellular transport.

Question 23

kinesins and dyneins

Answer 23

assoc with microtubules. vesicle transport. kinesin to positive end, such as to synapse of neuron.

Question 24

kinesin

Answer 24

aligning xsomes during metaphase. depolymerizing microtubules during anaphase.

Question 25

dynein

Answer 25

sliding movement of cilia and flagella. toward negative end of MT. Ex: waste and recycled NT toward soma.

Question 26

function of enzymes in catalyzing biological reactions

Answer 26

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.

Question 27

oxidoreductase

Answer 27

catalyze oxidation-reduction reactions. often have cofactor that acts as electron carrier.

Question 28

transferase

Answer 28

catalyze movement of functional group from one molecule to another. often called transferases, but also include kinase.

Question 29

hydrolase

Answer 29

breaking down of compound into two with addition of water. commonly named after substrate. examples are phosphatases, peptidases, nucleases, lipases.

Question 30

lyase

Answer 30

cleavage of one into two without water. reversible. often called synthetase in reverse.

Question 31

isomerase

Answer 31

rearrangement of bonds within a molecule. might also be classified as oxidoreductases, transferases, lyases. catalyze reations between constitutional AND stereoisomers

Question 32

LI'L HOT

Answer 32

ligase, isomerase, lyase, hydrolase, oxidoreductase, transferase

Question 33

ligase

Answer 33

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.

Question 34

active site model

Answer 34

no alteration of secondary or tertiary structure necessary upon binding of substrate

Question 35

induced fit

Answer 35

endergonic binding. exergonic letting go.

Question 36

cofactors

Answer 36

don't carry, but participate in reaction. inorganic.

Question 37

coenzyme

Answer 37

organic. often carrier. NAD+.

Question 38

prosthetic group

Answer 38

tightly bound coenzyme or cofactor

Question 39

apoenzyme

Answer 39

does not include cofactor

Question 40

vitamin

Answer 40

organic cofactors and coenzymes

Question 41

mineral

Answer 41

inorganic cofactors

Question 42

charge of DNA

Answer 42

negative

Question 43

temperature change, effect on enzyme

Answer 43

wrong geometry, misfolding