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Medical Biochemistry > Pre Knowledge (Chapters 2, 5, 12) > Flashcards

Pre Knowledge (Chapters 2, 5, 12) Flashcards

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USMLE® Step 1 flashcards
1
Q

(2) Proteins are polymers consisting of ..

A

amino acids

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2
Q

Proteins contain a wide range of … like alcohols, thiols, thioethers, carboxylic groups, amines and basic groups like amines

A

Functional groups

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3
Q

Components amino acid

A

central a carbon
R group (side chain)
amino group (NH2)
carboxyl group

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4
Q

Amino acids are chiral: explain

A

Mirror isomers: L isomer and D isomer.
Only L isomers are found in proteins

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5
Q

Zwitterions

A

Amino acids in solution at physiological pH have a dipolar form (NH3+ and COO-)

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6
Q

Hydrophobic / nonpolar amino acids

A

-Glycine, Gly, G
-Alanine, Ala, A
-Proline, Pro, P
- Valine, Val, V
- Leucine, Leu, L
- Isoleucine, Ile, I
- Methionine, Met, M
- Tryptophan, Trp, W
- Phenylalanine, Phe, F

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7
Q

polar uncharged amino acids

A
  • Serine, Ser, S
  • Threonine, Thr, T
  • Tyrosine, Tyr, Y
  • Asparagine, Asn, N
  • Glutamine, Gln, Q
  • Cysteine, Cys, C
  • Histidine, His, H
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8
Q

Polar positive amino acids

A
  • Lysine Lys, K
  • Arginine, Arg, R
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9
Q

Polar, negative amino acids

A
  • Aspartate, Asp, D
  • Glutamate, Glu, E
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10
Q

Peptide bond

A

C=O - NH

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11
Q

Most common cross-ink within the linear polypeptide chain

A

Disulfide bonds

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12
Q

Most peptide bonds have the … configuration

A

trans
> Steric repulsion, two atoms closer tha Van der Waals contact distance > opposing force

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13
Q

The alpha helix is stabilized by intrachain …

A

hydrogen bonds

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14
Q

Characteristics of globular proteins: enzymes, signaling molecules, regulatory proteins

A

-Lack of symmetry
-Solubility in water

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15
Q

Which motif is found in many DNA binding proteins

A

Helix-turn-helix

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16
Q

(2) motifs

A

Secondary structures frequently present in proteins

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17
Q

(5) Catalytically active RNA molecules

A

Ribozymes

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18
Q

Properties of enzymes are speed and specificity. Which enzymes catalyze proteolysis of peptide bonds?

A

Proteases

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19
Q

The six major classes of enzymes

A
  • Oxidoreductases: oxidation-reduction
  • Transferases: group transfer
  • Hydrolases: hydrolysis reactions (transfer of funcional groups of water)
  • Lyases: addition or removal of groups to form double bonds
  • Isomerases: isomerization (intramolecular group transfer)
  • Ligases: ligation of two substrates at the expense of ATP hydrolysis
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20
Q

Ester bond

A

C=O
-O

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21
Q

Kinase and phosphatase function

A

Kinase: phosphorylation
Phosphatase: de phosphorylation

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22
Q

Molecules which regulate activity of the enzyme

A

Cofactor

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23
Q

Groups of cofactors

A

-Coenzymes (small organic molecules)
-Metals

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24
Q

Tightly bound coenzymes which are unchanged in the overall chemical reaction

A

Prostethic groups
> loosly associated coenzymes often behave like second substrates (cosubstrates) > bound by enzyme, changed and released.

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25
Q

Enzyme without cofactor

A

Apoenzyme

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26
Q

Catalytically active enzyme with cofactor

A

Holoenzyme

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27
Q

A reaction can take place spontaneously if …

A

dG < 0

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28
Q

A system is at equilibrium if dG =

A

0

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29
Q

Endergonic reactions

A

dG > 0, input of energy needed (or coupling to energetically favourable reaction(s)

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30
Q

Does dG give information about the rate of reaction?

A

No

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31
Q

dG in A + B <=> C + D

A

dG = dG’0 RT ln([A][B]/[C][D])

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32
Q

How to measure dG0’

A

In equilibrium
dG0’ = -RT ln([A]eq[B]eq/[C]eq[D]eq)
because dG = 0

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33
Q

K’eq

A

= [A]eq[B]eq/[C]eq[D]eq
= e ^ -dG0’ / RT
RT = 2.48 at 298 K
pH = 7 in dG’0

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34
Q

Do enzymes alter the reaction rate? And the equilibrium?

A

Reaction rate: yes
Equilibrium: no
Equilibrium constants are the same with altered rate constants for foward and reverse reaction

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35
Q

What is the relative free energy of the transition state in a reaction?

A

Higher than that of subtrate and product.

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36
Q

Gibbs free energy difference between transition state and substrate

A

Activation energy.

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37
Q

An enzyme … the activation energy

A

lowers

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38
Q

Substrate-enzyme biding site mechanism

A

Induced fit

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39
Q

Free energy released during formation of large number of weak interactions between enzyme and substrate

A

Binding energy

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40
Q

Weak interaction

A

Ionic interactions, hydrogen bonds, Van der Waals interactions, Hydrophobic interactions/force

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41
Q

Km is the subtrate concentration at

A

1/2 * Vmax

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42
Q

A low Km means

A

High affinity of the enzyme for the substrate

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43
Q

Michaelis-Menten equation

A

v = Vmax * ([S]/[S] + Km)

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44
Q

Km equation

A

k-1+k2/k1
[E][S]/[ES]

45
Q

Lineweaver-Burk plot characteristics

A

Slope: Km/Vmax
x- Intercept: -1/Km
y- Intercept: 1/Vmax
Axes
x: 1/[S]
y: 1/v0

46
Q

Elasticity of the enzyme

A

The enzyme activity is sensitive to changes in environmental conditions (changes in [S])
- At [S] < Km: elastic but little activity
- At [S] > Km: active but inelastic.

47
Q

Vmax and k-cat (k2) equation

A

Vmax = k-cat*[E]tot
[E]tot = [E] + [ES]

48
Q

fraction of active site filled

A

f-es = V0/Vmax = [S]/([S]+Km)

49
Q

Specificity constant

A

k-cat/Km
V0 = (k-cat/Km) [S][E]tot

50
Q

Sequential reactions

A

All substrates must bind to the enzyme before any product is released.

51
Q

Types of sequential reactions

A

-Ordered sequential: all substrates must bind in defined sequence.
-Random sequential

52
Q

Double-displacement reactions

A

One or more products are releplaced before all substrates bind the enzyme

53
Q

Allosteric enzymes

A

Consist of multiple subunits and multiple active sites (binding sites), among one of them could be a allosteric actiation site
> no classic MM curve

54
Q

Temperature increases enzyme activity until

A

denaturation temperature

55
Q

Types of enzyme inhibitors

A

-Irreversible inhibitor
-Reversible inhibitors

56
Q

Types of reversible enzyme inhibitors

A

-Competitive inhibition
-Uncompetitive inhibition
-Noncompetitive inhibition

57
Q

Competitive inhibition

A

Inhibitor competes with the substrate for the enzyme
> has a higher affinity for the enzyme
> Only effective at low [S]
> If [S] increases, some [S] will bind nevertheless

58
Q

How are Vmax and Km changed with competitive inhibition

A

Increase of Km
Vmax stays the same

59
Q

Km after competitive inhibition

A

Ki (inhibitor) = [E][I]/[EI]

60
Q

Uncompetitive inhibition

A

Inhibitor binds only to the ES complex
- Substrate dependent
- Prevents catalysis rather than substrate binding
- Cannot be overcome by increasing [S]

61
Q

Km and Vmax after uncompetitive inhibition

A

Km lowered (Kmapp apparant Km)
Vmax lowered

62
Q

Changes in Lineweaver Burk plot in UC inhibition

A

Same slopes, different x and y intercepts (higher since Km and Vmax lowers)

63
Q

Noncompetitive inhibition

A

Inhibitor binds to different site than the substrate
- can bind free enzyme or ES complex, but decreases catalysis
- Cannot be overcome by increasing [S]

64
Q

Mixed NC inhibition

A

Noncompetitive inhibition in which the inhibitor binds to its binding site preferably to either the free or bound state of the enzyme to the substrate

65
Q

Km and Vmax after NC inhibition

A

Vmax lowered
Km not affected

66
Q

What are potent competitive inhibitors?

A

Transition-state analogs
> resemble transition state
> bind tightly to active binding site

67
Q

Irreversible inhibitors bind …

A

covalently

68
Q

Groups of irreversible enzyme inhibitors

A

-Group-specific reagents
-Affinity labels
-Suicide inhibitors

69
Q

group-specific reagents

A

inhibit enzymes by reacting with specific side chains of the enzyme
> not very specific

70
Q

Affinity labels (reactive substrate analogs)

A

Are structurally similar to the substrate and covalently bind to active site residues (catalytic site)
> more specific

71
Q

Suicide inhibitors

A

Also called mechanism based inhibitors
> use the mechanism of the enzyme to inhibit them, for example the enzyme changes the inhibitor into a reactive molecule which reacts with catalytic residues covalently.
- The enzyme commits suicide by generating its own inhibition

72
Q

Molecular mechanism penicillin

A

Suicide inhibitor
- For the gram positive S aurus which has 1 membrane and a cell wall of peptidoglycans with crosslinks facilitated by glycopeptide transpeptidase (transfers peptide bond)
- penicillin has a beta-lactam ring which resembles the transition state of the transpeptidase reacion (R-D-ala-D-Ala) and has a peptide bond (reactive). And penicillin covalently binds the catalytic serine residue.

73
Q

(12) Characteristics fatty acids

A

Long hydrocarbon chain with carboxylic acid groups

74
Q

Saturated fatty acids have … double bonds

A

No

75
Q

Lipid bilayer membranes contain carbohydrates bound to…

A

proteins or lipids

76
Q

Membrane protein types

A
  • Pumps
  • Channels
  • Receptors
  • Energy transducers
  • Enzymes
77
Q

Membranes are …. assemblies (covalent/noncovalent)

A

noncovalent -> hydrophobic interactions

78
Q

Membranes are (a)symmetric

A

asymmetric

79
Q

Phospholipid components

A

-One or more fatty acids
-Platform to which fatty acids are attached (like glycerol)
-A phosphate
-An alcohol attached to the phosphate

80
Q

How are phospholipids with a glycerol platform called?

A

Phosphoglycerides, bound to two FAs and a phosphorylated alcohol.

81
Q

Bonds between glycerol and fatty acids

A

ester bonds formed by condensation of hydroxyl groups of glycerol and carboxyl groups of the FAs.

82
Q

Sphingomyelin is a phospholipid in membranes derived from

A

a backbone of sphingosine (amino acohol with long unsaturated carbohydrate chain)

83
Q

Second class of membrane lipids: glycolipids. Characteristics

A
  • derived from sphingosine
  • amino group bound to FA
  • unit linked to the primary hydroxyl group is a glucose or galactose (instead of phosphorylcholine in sphingomyelin) with a ester linkage.
84
Q

Third major type of membrane lipids beside phospholipids and glycolipids

A

Cholesterol

85
Q

Structure cholesterol

A

-Four carbon rings sterol
- At one end: hydrocarbon tail
- other end: hydroxyl group which can interact with head group of phospholipids since it lays parallel to it in membrane

86
Q

Membrane lipids important characteristic in solubility

A

Amphipathic: hydrophilic head group and hydrophobic tail group. –> fatty acids lay parallel to each other.

87
Q

Micelle

A

globular structure formed from ionized fatty acids with single tails due to hydrophobic interactions in water.

88
Q

Two opposing sheets of a lipid bilayer are called:

A

leaflets

89
Q

lipid bilayers form …

A

spntaneously.

90
Q

Forces in spontaneous bimolecular sheet formation

A

-Hydrophobic interactions
-Vanderwaals attractive forces favor tails laying close to each other
- Electrostatc and hydrogen bonding between polar head groups and water molecules

91
Q

Lipid vesicles / liposomes

A

Aqueous compartments surrounded by a lipid bilayer
> can be synthesized artificially containing ions or molecules

92
Q

Why does tryptophan, a zwitterion, transfer through a lipid bilayer (without transporter or channel) faster than K+ or Na+

A

It is amphipathic instead of solely hydrophilic

93
Q

Myelin (membrane around neurons) contain many/little protein

A

little, it is a lipid rich membrane > form electrical insulator

94
Q

Plasma membrane consist approximately …% of proteins

A

50%

95
Q

Membranes with most proteins

A

mitochondria and chloroplasts (energy transduction membranes)

96
Q

Classes of membrane proteins

A
  • Integral membrane proteins: interact extensively with hydrocarbon chains of membrane lipids > only released by agents which compete with the nonpolar interactions
  • Peripheral membrane proteins: bound to membrane with primarily electrostatic interactions and hydrogen bonds
97
Q

Most common structural transmembrane motif

A

Membrane-spanning alpha helices

98
Q

A beta barrel of beta strands can form a …

A

channel protein, alternating hydrophobic and hydrophilic amino acids along each beta strand

99
Q

Prostaglandin H2 synthase is a integral membrane protein. How is it attached?

A

With a set of alpha helices with hydrophobic side chains on the outside of the surface to hydrophobically interact with the fatty acid tails

100
Q

Which reaction is catalyzed by prostaglandin H2 synthase

A

Arachidonic acid (lipid) > prostaglandin G2 (by the cyclooxygenase (COX)) > prostaglandin H2 (by the peroxidase (POX))

101
Q

How does aspirin lower inflammatory response, fever and pain

A

It covalently links its acetyl group (acetylsalicyclic acid) to a serine residue along the hydrophobic channel (with more hydrophobic interaction force than the lipid bilayer to catch the substrate btw) to block the channel irreversibly (no suicide inhibitor, not the catalytic residue)
> The COX cannot function and prostaglandin H2 is not synthesized, prostaglandins promote inflammatory response, including swelling, pain and fever.

102
Q

How does ibuprofen inhibit prostaglandin H2 synthase? What type of inhibitor is it?

A

Ibuprofen is a competitive inhibitor which blocks the hydrophobic channel.

103
Q

Lateral movement of membrane proteins and lipids

A

lateral diffusion

104
Q

Lateral diffusion speed and transverse diffusion speed of lipids

A

Lateral diffusion: rapid
Transverse diffusion (flipflop): very slow (catalyzed by enzymes)

105
Q

Membrane fluidity is dependent on

A
  • Fatty acid composition
    -Cholesterol content
106
Q

Which FAs induce a more fluid membrane?

A

Unsaturated, less Van der Waals force.

107
Q

Cholesterol makes the membrane more fluid/solid

A

solid, forms hydrogen bonds with carbonyl oxygen atom of phospholipid head group and hydrocarbon tail of cholesterol is located in nonpolar core of the bilayer

108
Q

Do long or short FAs increase fluidity of a membrane

A

Small FAs: less Vanderwaals interactions

109
Q
A

Medical Biochemistry (2 decks)

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