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LO MCAT BIOCHEM > CH 4: AAs and Proteins > Flashcards

CH 4: AAs and Proteins Flashcards

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MCAT flashcards
1
Q

What are proteins?

A

Macromolecules

Purpose: enzymes, hormones, receptros, channels, transporters, antibodies, and support

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2
Q

Why are side chains unique?

A

Variable R-group

Influence AA physical and chemical properties

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3
Q

What are the 2 Acidic/Hydrophilic AAs?

A

Aspartic acid (Asp) D
Glutamic Acid (Glu) E

E comes after D

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4
Q

What are the 3 Basic/Hydrophilic AAs?

A

HIstory of ARGentina was a LY

Lysine (Lys) K
Arginine (Arg) R
Histidine (His) H: “His goes both ways” proton donor or acceptor

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5
Q

What are the 9 HydroPHOBIC/NONpolar AAs?

A
  1. Glycine (Gly) G
  2. Alanine (Ala) A
  3. Valine (Val) V
  4. Leucine (Leu) L
  5. Isoleucine (Ile) I
  6. Phenylalanine (Phe) F
  7. Tryptophan (Trp) W
  8. Methionine (Met) M
  9. Proline (Pro) P

Phenylalanine and Tryptophan are aromatic

1st five: aliphatic (alkyl)

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6
Q

What are the 6 Polar/Hydrophilic AAs?
Neutral

A

STY CNQ
1. Serine (Ser) S
2. Threonine (Thr) T
3. Tyrosine (Tyr) Y
4. Asparagine (Asn) N
5. Glutamine (Gln) Q
6. Cysteine (Cys) C

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7
Q

What are the 2 sulfur-containing AAs?

A
  1. Cysteine (Cys) C: POLAR
  2. Methionine (Met) M: NONPOLAR
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8
Q

Why is Proline (Pro) P unique

A

Its amino group is covalently bound ot NP side chain

This forms a secondary alpha-amino structure and ring

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9
Q

What are the 9 essential AAs

A

PVT TIM HaLL
1. Lysine (Lys) K
2. Histidine (His) H
3. Threonine (Thr) T
4. Valine (Val) V
5. Leucine (Leu) L
6. Isoleucine (Ile) I
7. Phenylananine (Phe) F
8. Tryptophan (Trp) W
9. Methionine (Met) M

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10
Q

Which of the following AAs are most likely to be found on the exterior of a protein at pH 7.0
1. Leucine (Leu) L
2. Alanine (Ala) A
3. Serine (Ser) S
4. Isoleucine (Ile) I

A
  1. Serine POLAR
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11
Q

Amphoteric

A

Includes all AAs

Can act as acids of bases

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12
Q

Henderson-Hasselbalch Equation

A

Relationship bw pH, pKa, and equilibrium in acid-base rxn

pH= pKa + log ([A-]/[HA]) = pKa = log([base form]/[acid form])

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13
Q

When the pH of the solution is LESS than the pKa of an acidic group, the acidic group will mostly be in its…

A

protonated form

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14
Q

When the pH of the solution is GREATER than the pKa of an acidic group, the acidic group will mostly be in its…

A

DEprotonated form

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15
Q

Which functional group of AAs has a stronger tendency to donate protons: carboxyl groups (pKa = 2.0) or ammonium groups (pKa = 9)?
Which group will donate protons at the lowest pH (highest [H+])?

A

HIGH pKa = weak acid
LOW pKa = strong acid and DEprotonate easier

Carboxyl group

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16
Q

Ammonium group

A

Protonated (AKA acidic) form of an amine

pKa bw 9-10

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17
Q

Zwitterion

A

Molecule w positive and negative charges that balance

AKA dipole ion

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18
Q

Isoelectric point (pI)

A

pH at which a molecule is uncharged (zwitterionic)

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19
Q

Peptide bonds

A

Covalent bonds that link AA together into polypeptide chains

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20
Q

Disulfide Bridges

A

Covalent bonds bw cysteine R-groups

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21
Q

Backbone

A

NCCNCC pattern formed from AAs in polypeptides

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22
Q

Residue

A

Refers to individual AAs when part of polypeptide chain

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23
Q

Proteolysis or Proteolytic cleavage

A

Hydrolysis of protein by another protein

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24
Q

Proteolytic Enzyme or Protease

A

Protein that does cutting

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25
Q

Denatured

A

Improperly folded, non-functional proteins

Disrupt protein shape WO breaking peptide bonds

Can occur dt:
1. Urea (H-bonds)
2. pH extremes
3. Temperature extremes
4. Salt concentration (tonicity)

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26
Q

Primary Structure

A

AA order in polypeptide chain

Bond: peptide

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27
Q

Secondary Structure

A

Initial folding of polypeptide chain

a-helix and B-pleated sheet

Bonds: H-bonds,

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28
Q

What are the 2 types of B-pleated sheets

A

parallel and antiparallel

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29
Q

Tertiary Structure

A

Interactions bw AA residues located more distantly in the polypeptide chain

Bonds/interactions: hydrophobic/hydrophilic interactions
1. (N-C) van der Waals forces bw NP side chains
2. (N-C)H-bonds bw polar side chains
3. (Cov) Disulfide bonds bw cysteine residues
4. (N-C) Electrostatic interactions bw acidic and basic side chains

30
Q

Hydrophobic Effect

A

HydroPHOBIC R-groups fold into interior of protein while hydroPHILIC R-groups are exposed to water on surface of protein

31
Q

Quaternary Structure

A

Interaction bw polypeptide subunits

Bonds/interactions: same as tertiary
NO peptide bond involvement

32
Q

Reaction coupling

A

A favorable rxn used to drive an unfavorable one

Possible dt additive free energy changes

33
Q

Hydrolase

A

HYDROlyses (AKA breaks) chemical bonds

includes ATPases, proteases, etc

34
Q

Isomerase

A

rearranges bonds win a molecule to form an ISOMER

35
Q

Ligase

A

forms a chemical bond

EX: DNA ligase

36
Q

Lyase

A

BREAKS chemical bonds

NOT BY oxidation or hydrolysis

EX: pyruvate decarboxylase

37
Q

Kinase

A

transfers P group to a molecule from a HIGH energy carrier like ATP

EX: phosphofructokinase (PFK)

38
Q

Oxidoreductase

A

runs redox rxns

EX: oxidases, reductases, dehydrogenases, etc

39
Q

Polymerase

A

polymerization: addition of nucleotides to the leading strand of DNA by DNA polymerase III

40
Q

Phosphatase

A

removes P group from a molecule

41
Q

Phosphorylase

A

transfers P group to a molecule from inorganic phosphate

EX: glycogen phosphorylase

42
Q

Protease

A

hydrolyzes peptide bonds

EX: trypsin, chymotrypsin, pepsin

43
Q

Active site

A

region in an enzyme that’s directly involved in catalysis

44
Q

Active site

A

region in an enzyme that’s directly involved in catalysis

45
Q

Substrates

A

reactants in an enzyme catalyzed rxn

46
Q

Active site model

A

AKA “lock and key hypothesis”

States: substrate and active site are perfectly complementary

47
Q

Induced fit model

A

Substrate and active site differ SLIGHTLY in structure

Binding of the substrate induce conformational change in enzyme

48
Q

Protease Active site

A

Protein cleaving

Active site has serine residue
OH group is NUC and attacks carbonyl C of an AA residue in polypeptide chain

49
Q

Recognition Pocket

A

Usually found in proteases

Pocket in structure that attracts certain residues on substrate polypeptides

50
Q

Cofactors

A

Metal ions or small molecules (not proteins)

Required for activity in many enzymes

51
Q

Coenzyme

A

Organic molecule cofactor

Bind to substrate during the catalyzed reaction

52
Q

Covalent Modification

A

Proteins can have diff groups covalently attached to them

Regulates activity, lifespan, and location

EX: P from ATP by protein kinase to hydroxyl of serine, threonine, or tyrosine
Phosphorylation either in/activates enzyme

Protein phosphorylases use INorganic phosphate INSTEAD of ATP

Protein phosphatases reverse phosphorylation

53
Q

Proteolytic Cleavage

A

many enzymes/proteins synthesized in inactive forms (AKA zymogens)

Activated by cleavage by a protease

54
Q

Consitutive Activity

A

When proteins show continuous rapid catalysis if their regulatory subunit is removed

55
Q

Allosteric Regulation

A

Modification of active-site activity thru interactions of molecules w other specific sites on the enzyme

Noncovalent and reversible

Can increase or decrease catalysis

56
Q

Feedback Inhibition (AKA negative feedback)

A

End product shuts off enzyme eaerlier in pathway

57
Q

Feedforward Stimulation

A

Stimulation of enzyme by substrate or molecule used in synthesis of the substrate

58
Q

Enzyme kinetics

A

Rate of formaiton of products from substrates in presence of enzyme

59
Q

Reaction rate (V)

A

amt of product formed per unit time

mol/s

depends on substrate concentration [S] and enzyme

60
Q

Saturated (Vmax)

A

when theres so much substrate that every active site is continuously occupied and adding more substrate doesn’t increase the reaction rate

61
Q

Michaelis constant (Km)

A

substrate concentration where reaction velocity is half its max

Formula: Vmax/2

62
Q

Positive Cooperativity

A

binding of substrate to one subunit increases the affinity of the other subunits for substrate

63
Q

Negative Cooperativity

A

binding of substrate to one subunit reduces the affinity of other subunits for substrate

64
Q

Competitive Inhibition

A

molecules compete w substrate for binding st active site

inhibition can be overcome by adding more substrate
then can outcompete the inhibitor (Vmx NOT affected)

can get to the same Vmax but takes more substrate (INCR Km)

Vmax NO change; Km INCR

65
Q

Noncompetitive Inhibitors

A

Bind at allosteric site NOT active site

Amt of substrate added DOES NOT displace inhibitor from site (DECR Vmax)

Also affects Vmax/2

DOES NOT affect Km since substrate can still bind to active site BUT inhibitor prevents catalytic activity of the enzyme

Vmax DECR; Km NO change

66
Q

Uncompetitive Inhibitor

A

Inhibitor only able to bind to the enzyme-subtrate complex

Bind to allosteric sites (like noncompetitive inh)

DECR Vmax (limit amt of E-S complex converted to product) and DECR Km

Vmax DECR; Km DECR

67
Q

Mixed type inhibition

A

Inhibitor can bind to EITHER unoccupied enzyme of E-S complex

Km INCR
if enzyme has GREATER affinity for the inhibitor in free form

Km DECR
if E-S complex has greater affinity for inhibitor

if there’s EQUAL affinity in both forms–> actually noncompetitive

Vmax DECR; Km varies

68
Q

Lineweaver-burk slope

A

Km/Vmax

69
Q

lineweaver-burk y-int

A

1/Vmax

70
Q

lineweaver-burk x-int

A

-1/Km

LO MCAT BIOCHEM (2 decks)

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