O-Chem, Proteomics, Enzymes Flashcards Preview

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Flashcards in O-Chem, Proteomics, Enzymes Deck (54):
1

Identification of carbon atoms in an organic compound

Carbons are numbered starting from the most oxidized carbon-containing group with numbers or greek letters

2

reactions are classified according

to the functional groups that react

3

LEO (lion) goes GER

loses electrons oxidizes
gains electrons reduces

4

quaternary amine structure

-R1-N+[-R2][-R3][-R4], -CH2-[N+(CH3)3]

5

H2O molarity

55.5 M
extent of dissociation is not appreciable

6

ion product of H2O

K-w = {H+][OH-] = 1x10^-14
fure pure water [H+] = [OH-] = 1x10^-7

7

The Henderson-Hasselbalch equation

pH = pK + log10([A-]/[HA])

8

carbonic acid buffering

CO2 + H2O H2CO3 H+ + HCO3-

9

normal pH range of arterial blood

7.37 to 7.43

10

(amino acids/peptide bonds)
Nonpolar, aliphatic amino acids

glycine [(gly, G) -H], alanine [(ala, A) -CH3], proline [(pro, P) -CH2CH2CH2-], valine [(val, V) -CH3(CH3)2], leucine [(leu, L) -CH2CH(CH3)2], isoleucine [(ile, I) -[CH(CH3)]CH2CH3]

11

(amino acids/peptide bonds)
Amino acids are usually of the _____ configuration

L-configuration

12

(amino acids/peptide bonds)
Amino acids usually contain ____, _____, and ______, all bonded to the _______.
Exceptions are ______ and ______.

carboxyl group, amino group, side chain, α-carbon atom
glycine, proline

13

(amino acids/peptide bonds)
At physiologic pH, they carry a ______ charge on their amino groups and a _____ charge on their carboxyl groups.

positive, negative

14

(amino acids/peptide bonds)
Aromatic amino acids

Nonpolar - Phenylalanine (phe, F)
More Polar - tyrosine (tyr, Y), tryptophan (trp, W)

15

(amino acids/peptide bonds)
Polar, uncharged amino acids

asparagine [(asn, N) -CH2(C=O)NH2], glutamine [(gln, Q) -CH2CH2(C=O)NH2], serine [(ser, S) -CH2OH], threonine [(thr, T) - CH(OHCH3)]

16

(amino acids/peptide bonds)
Sulfur-containing

Methionine [(met, M) -CH2CH2SCH3], cysteine [(cys, C) -CH2SH]

17

(amino acids/peptide bonds)
Charged, negative (acidic)

Aspartate (asp, D), glutamate (glu, E)

18

(amio acids/peptide bonds)
charged, positive (basic)

arginine (arg, R), lysine (lys, K), histidine (his, H)

19

all of the 20 amino acids except _____ are of the L-configuration.

glycine

20

classification of amino acids is based upon ...

side chains

21

(charges on amino acids)
At physiologic pH, the α-amino group ____

are protonated (pKa ~ 9), carries a positive charge

22

(charges on amino acids)
At physiologic pH, the carboxyl group ____

is dissociated (pKa ~ 2) and carries a negative charge

23

(charges, amino acids)
The isoelectric point (PI)

is the pH at which the number of positive charges equals the number of negative charges, and the overall charge on the amino acid is zero.

24

(pKa) aspartate

CH2-COOH CH2COO- + H+

25

(pKa) glutamate

CH2-CH2-COOH CH2-CH2-COO- + H+

26

(pKa) histidine

6.0

27

(pKa) cysteine

CH2SH CH2S- + H+

28

(pKa) tyrosine

CHs-benzene-OH CH2-benzene-O- + H+

29

(pKa) lysine

CH2-CH2-CH2-CH2-NH3 CH2-CH2-CH2-CH2-NH2 + H+

30

(pKa) arginine

CH2-CH2-CH2-NH-C(NH2)2 CH2-CH2-CH2-CH2-C(=NH)NH2 + H+

31

(protein structure)
describe denaturation

such agents as heat and urea cause unfolding of polypeptide chains without hydrolyzing peptide bonds. Denaturation destroys 2ndary, 3rdary structures without affecting the primary structure.

32

(protein structure)
describe renaturation

if the denatured protein returns to its native state after the denaturing agent is removed, it is renatured.

33

(protein structure)
describe - posttranslational modifications

Occurs after the protein has been synthesized on the ribosome.
Phosphorylation, glycosylation, ADP ribosylation, methylation, hydroxylation and acetylation affect the charge and the interactions between amino acid residues -> alters 3D shape -> alters the function.

34

(protein structure)
Adult hemoglobin (___) consists of _______ (________), each containing a molecule of _____.

(HbA), four polypeptide chains (two α-chains and β-chains), heme

35

(protein structure)
hemoglobin - _____ of α-helix occur in each chain, labeled _________

eight regions, A through H

36

(protein structure)
hemoglobin - ____ fits into a crevice in each globin chain and interacts with ________

heme, two histidine residues

37

(protein structure)
hemoglobin - function, general

carries oxygen from the lungs to the tissues, and returns CO2 and protons from the tissues to the lungs.

38

(protein structure)
hemoglobin - positive cooperativity

Binding of O2 to one heme group in hemoglobin increases the affinity for O2 of its other heme groups, creating the sigmoidal behavior of the oxygen saturation curve.

39

Enzymes facilitate biochemical reactions by ...

reducing the Gibbs free energy of activation, ΔG, making it easier for the reaction to reach its transition state.

40

The actives sites of enzymes are the regions where _____ bind and are ...

substrates, converted to products, which are released.

41

(define)
competitive inhibitors

Blocking of the action of an enzyme by a compound that binds to the free enzyme, preventing the substrate from binding and thus preventing the substrate from binding and thus preventing the enzyme from acting on that substrate. Saturating concentrations of substrate can remove the inhibition.

42

(define)
noncompetitve inhibitors

Inhibition of enzyme activity by substances that combine with the enzyme at a site other than that utilized by the substrate.

43

allosteric enzymes

Bind activators or inhibitors at sites other than the active site. Plots of the velocity-versus-substrate concentration for allosteric enzymes produce curves that are sigmoidal

44

Dependence of velocity on [E], [S], temperature, and pH

The velocity of a reaction, ν, increases with the enzyme concentration, [E], if the substrate concentration, [S], is constant.

45

(enzymes)
If [E] enzyme concentration is constant, ν, velocity ...

increases with [S] substrate concentration until the maximum velocity, Vmax is attained.

46

(enzymes)
at Vmax, maximum velocity ...

all active sites of the enzymes are saturated with substrate

47

The velocity of an enzymatic reaction ____ with ____ until _____ is reached, after which the velocity ____ due to ______

increases, temperature, maximum, decreases, the denaturation of the enzyme

48

Each enzyme-catalyic reaction has an optimal pH. Too high or too low a ph can cause _______

denaturation

49

(enzymes)
Michaelis-Menten equation

V = (Vmax [S]) / (Km + [S])
Km = (k2 + k3) / k1

50

(enzymes)
Michaelis-Menten equation - Km

Km is the substrate concentration at which v = (1/2) Vmax

51

Competitive inhibition is reversed by

increasing the substrate concentration [S]

52

Pyruvate dehydrogenase and glycogen synthase are inhibited by ________

phosphorylation

53

Glycogen phosphorylase is activated by ______

phosphorylation

54

Isoenzymes or isozymes are ...

enzymes that catalyze the same reaction, but differ in their amino acid sequence and, therefore, in many of their properties