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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What are the properties of water?

A

proton donor and acceptor, high boiling and melting point, cooperative binding, and large surface tension

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2
Q

What is water a good solvent for?

A

charged and polar substances such as AA and peptides, small alcohols and carbs

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3
Q

What is water a bad solvent for?

A

nonpolar substances such as aromatic moieties, and aliphatic chains

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4
Q

What are usual hydrogen acceptors?

A

oxygen and nitrogen

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5
Q

What are components of van der Waals interactions?

A 
Attractive force (London dispersion) depends on the polarizability; will attract at longer distances
Repulsive force (Steric repulsion)  depends on the size of atoms; will repulse at shorter distances
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6
Q

hydrophobicity and entropy

A

Low entropy is thermodynamically unfavorable, thus hydrophobic solutes have low solubility because they are highly order and have less room to move around

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7
Q

What are the colligative properties of water?

A

Boiling point, melting point, and osmolarity; Do not depend on the nature of the solute, just the concentration

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8
Q

What are the non-colligative properties of water?

A

Viscosity, surface tension, taste, and color; Depend on the chemical nature of the solute

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9
Q

What is osmosis?

A

Water moves from areas of high water concentration (low solute concentration) to areas of low water concentration (high solute concentration).

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10
Q

What is isotonic?

A

Solutions of equal osmolarity; no water movement

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11
Q

What is hypertonic?

A

Higher osmolarity than the cell; water moves out and cell shrinks

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12
Q

What is hypotonic?

A

Lower osmolarity than the cell; water moves in and cell swells

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13
Q

What are the products of ionization of water?

A

Products are a proton (H+) and a hydroxide ion (OH–)

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14
Q

proton hydration

A

Protons do not exist free in solution, They are immediately hydrated to form hydronium (oxonium) ions (H3O+).

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15
Q

What is hydronium?

A

a water molecule with a proton associated with one of the non-bonding electron pairs.
Hydronium ions give up a proton to a nearby water molecules.

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16
Q

What is the Equilibrium Constant?

A

Equilibrium constant tells us the point in a reversible reaction where the rate of product formation equals the rate of product breakdown to starting reactants.

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17
Q

What is pH?

A

pH is defined as the negative logarithm of the hydrogen ion concentration
pH = -log[H+]; 1 unit = 10 folds

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18
Q

What is a strong base and acid?

A 
Strong acid (proton donor) = hydrochloric or acetic acid
Strong base (proton acceptor) = Sodium hydroxide
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19
Q

pKa

A

pKa = log 1/Ka = -log Ka

The stronger the tendency to dissociate a proton, the stronger the acid and the lower the pKa

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20
Q

What is titrations?

A 
Taking a fully protonated  molecule and add base to see when you will start losing protons 
Mid point (pI) - presents  the pH when you have 100% net change of zero
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21
Q

What is a buffer?

A

Aqueous systems that tend to resist changes in pH. Generally around the pKa

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22
Q

What is an enantiomer?

A

nonsuperposable mirror images of each other

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23
Q

What are the nonpolar, aliphatic AA?

A 
Glycine (Gly, G)
Alanine (Ala, A)
Proline (Pro, P)
Valine (Val, V)
Leucine (Leu, L)
Methionine (Met, M)
Isoleucine (Ile, I)
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24
Q

What are the aromatic AA?

A

phenylalanine (Phe, F)
tyrosine (Tyr, Y)
tryptophan (Trp, W)
These amino acid side chains absorb UV light at 270–280 nm

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25
Q

What are the polar, uncharged aliphatic AA?

A 
Serine (Ser, S)
Threonine (Thr, T) 
Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)
These amino acids side chains can form hydrogen bonds. Cysteine can form disulfide bonds to become Cystine.
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26
Q

What are the positively charged aliphatic AA?

A

Lysine (Lys, K), Arginine (Arg, R) and Histidine (His, H)

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27
Q

What are the negatively charged aliphatic AA?

A

Aspartate (Asp, D) and Glutamate (Glu, E)

These AA are Acidic because they have already donated their proton

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28
Q

What is a Zwitterion?

A

the amino and carboxyl groups are both ionized. This allows amino acids to act as both acids and bases.

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29
Q

What is the difference between cation and anion?

A

Cation - Positively charged, and you’re attracted to a cathode (negative)
anion – negatively charged ion that migrates to anodes

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30
Q

What is the use of chromatography?

A

Chromatography is commonly used for preparative separation in which the protein is often able to remain fully folded.

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31
Q

What is column chromatography?

A

Column chromatography allows separation of a mixture of proteins over a solid phase (porous matrix) using a liquid phase to mobilize the proteins.
Proteins with a lower affinity for the solid phase will wash off first; proteins with higher affinity will retain on the column longer and wash off later.

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32
Q

What is ion-exchange chromatography?

A

Separation is based on charge –> Protein with net negative charge will move more slowly in a anion exchange matrix, and Protein with net positive charge will move more slowly in a cation exchange matrix

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33
Q

What is size exclusion/gel filtration chromatography?

A

Large proteins come out first - Too big to enter the pores in the beads.
Smaller out later - Enter cavities, migrate through column slower

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34
Q

What is affinity chromatography?

A

Separation based on binding affinity of the protein.
The matrix has chemical groups (ligands) covalently attached that Binds to a protein
Protein has affinity for the chemical group and is retained on column

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35
Q

What are the various types of protein structures?

A

Primary structure: The amino acid sequence of a protein.
Secondary structure: The local spatial arrangements of amino acids in proteins, such as the a-helix and b-sheet.
Tertiary structure: The three-dimensional structure of a protein.
Quaternary Structure: The combination of different proteins to form a complex through noncovalent interactions.

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36
Q

What is the point of resonance in peptide bonds?

A

The resonance causes the peptide bonds to be less reactive compared to esters, for example to be quite rigid and nearly planar, and to exhibit a large dipole moment in the favored trans configuration

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37
Q

What is the formation of the alpha-helix?

A

It is a right-handed helix with 3.6 residues (5.4 Å) per turn.
Peptide bonds are aligned roughly parallel with the helical axis.
Side chains point out and are roughly perpendicular with the helical axis.

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38
Q

Destabilizing alpha-helix

A

Blocks of Glu or Lys, or Arg - Charges repel each other
Asn, Ser, Thr and Cys - Bulk and shape can interfere if too close to together.
Pro is too rigid to be part of a helix; Gly has too much flexibility. Blocks of Gly tend to make a coil.

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39
Q

What are the constraints on alpha-helix?

A

Electrostatic repulsion based on the same charge
Bulkiness of R groups
Interaction between R groups spaced 3-4 residues apart.
Presence of Glycine or Proline
Amino acids at the amino and carboxyl terminus

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40
Q

What is the directionality in a parallel beta-sheet?

A

In parallel beta sheets, the H-bonded strands run in the same direction. Hydrogen bonds between strands are bent (weaker).

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41
Q

What is the directionality in a anti-parallel beta-sheet?

A

In antiparallel beta sheets, the H-bonded strands run in opposite directions. Hydrogen bonds between strands are linear (stronger).

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42
Q

What is the difference between a Beta loop and a beta turn?

A

Prolines and glycine are great for turns.

Loop are bigger than turns and can turn on the outside also. In a loop you will Glutamates and Aspartate

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43
Q

What is a beta turn?

A

beta turns occur frequently whenever strands in beta sheets change the direction
The 180° turn is accomplished over four amino acids
Proline in position 2 or glycine in position 3 are common in beta turns

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44
Q

What is a tertiary protein structure?

A

Tertiary structure refers to the overall spatial arrangement of atoms in a protein
Stabilized by numerous weak interactions between amino acid side chains - Largely hydrophobic and polar interactions; Can be stabilized by disulfide bonds
Two major classes: fibrous and globular (water or lipid soluble)

45
Q

What is a fibrous protein?

A

Fibrous proteins that have polypeptide chains arranged in long strands or sheets.
Supply support, structure and external protection.

46
Q

What is a globuar protein?

A

Globular proteins that have their polypeptide chains folded into a spherical or globular shape; Generally enzymes

47
Q

Secondary structures of fibrous protiens

A

alpha helix/disulfide bonds - keratin
beta confirmations - silk fibroin
triple helix - collagen

48
Q

How is alpha-keratin formed?

A

Hair α-keratin is an elongated α helix held by disulfide bonds.
Pairs of these helices are interwound in a left-handed sense to form two-chain coiled coils.
These then combine in higher-order structures called protofilaments and protofibrils.
About four protofibrils—32 strands of α-keratin in all—combine to form an intermediate filament.

49
Q

How is the structure of collagen formed?

A

Each collagen chain is a long Gly- and Pro-rich left-handed helix.
Three collagen chains intertwine into a right-handed superhelical triple helix.
Many triple-helices assemble into a collagen fibril.

50
Q

What is collagen?

A

Collagen is an important constituent of connective tissue: tendons, cartilage, bones, cornea of the eye.

51
Q

What is the role of 4-Hydroxyproline in collagen?

A

Forces the proline ring into a favorable pucker, and also Offers more hydrogen bonds between the three strands of collagen

52
Q

What are the defects of collagen?

A

Substitution of Cys or Ser for Gly at a single point in each a-chain can result in lethal conditions such as osteogenesis imperfecta (abnormal bone formation) and Ehlers-Danlos syndrome (loose joints).
Osteoarthritis can result from over expression of an incorrect collagen variant.

53
Q

Where are silk fibroins from?

A

Fibroin is the main protein in silk from moths and spiders

54
Q

What is silk fibroins made of?

A

Antiparallel beta-sheet structure and Small side chains (Ala and Gly) allow the close packing of sheets
The structure is stabilized by hydrogen bonding within sheets

55
Q

What are examples of globular proteins?

A

Enzymes, transport proteins, immunoglobulins

56
Q

What are globular proteins made of?

A

Globular proteins are composed of different motifs (alpha helix and beta loops and barrels) folded together

57
Q

What are quaternary structures?

A

The association of multiple polypeptide subunits into larger functional clusters

58
Q

How does a ligand bind?

A

The ligand binds to its binding site via noncovalent interactions that dictate protein structure and this allows the interactions to be transient

59
Q

How can proteins change their conformation?

A

Binding of ligand, Induced fit. Change in one subunit can affect the rest of protein, and Interactions between ligand and protein may be regulated.

60
Q

What is Ka?

A

Measurement of the affinity of a ligand for the protein.
A high Ka = a higher affinity for the protein.
Ka [L] = [PL]/[P]

61
Q

What is an induced fit?

A

Induced fit is when conformational change occurs in the ligand or protein upon the ligand binding and it allows for tighter binding of the ligand and for high affinity for different ligands

62
Q

What is the lock-and-key model?

A

The Lock and Key model assumes that complementary surfaces are preformed. Complementary in: size, shape, charge, hydrophobic/hydrophilic character

63
Q

What are the biological problems of O2 binding?

A

Protein side chains lack affinity for O2.

Some transition metals bind O2 well but would generate free radicals if free in solution

64
Q

What is the difference between myoglobin and hemoglobin?

A

Myoglobin (storage) Facilitates oxygen diffusion in muscle, only has 1 subunit (tertiary)
hemoglobin (transport) can bind oxygen via a protein-bound heme, is a tetramer of 2 subunits that binds 4 heme (quaternary)

65
Q

Why does CO binds better to heme than O2?

A

CO binds heme over 20,000 times better than O2 because the carbon in CO has a filled lone electron pair that can be donated to vacant d-orbitals on the Fe2+.

66
Q

What is the difference between T and R state?

A

T = Tense state, More interactions, more stable
-Lower affinity for O2

R = Relaxed state, Fewer Interactions, more flexible
-Higher affinity for O2

67
Q

What happens when the T state binds oxygen?

A

O2 binding triggers a T -> R conformational change

Conformational change from the T state to the R state involves breaking ion pairs between the α1-beta2 interface

68
Q

What is an Allosteric Protein?

A

Binding of ligand to one site affects the binding properties of another site of the same protein

69
Q

When does modulation occur?

A

occurs when ligand changes confirmation

70
Q

How is O2 released in the capillaries?

A

H+
CO2
Cl-
BPG

71
Q

How is proton binding related to O2 binding in hemoglobin?

A

Inversely related to the binding of O2

  • High O2 = bind O2, release protons (Lungs)
  • Low O2 = bind protons, release O2
72
Q

What is the Bohr Effect?

A

lowering pH (higher protons) decreases O2 affinity and HB binds to H+ in the peripheral tissues and transports it to the lungs

73
Q

What is the binding of Hb and CO2?

A

when CO2 is high, affinity for O2 decrease, and O2 released

In the Lungs O2 high, and thus, CO2 is released

74
Q

How is the charge of erythrocytes balanced?

A

Cl- enters the blood and binds to the N-terminus of the alpha subunit, lowering its pK and promoting H+ binding.
Cl- also forms a salt bridge with Arg 141-alpha, which promotes the T state of Hb.

75
Q

What is the role of BPG?

A

It is a Heterotrophic allosteric modulation which Binds at a distant site and Regulates O2-binding affinity by only allowing one molecule to bind per tetramer and Stabilizing the T state.

76
Q

What causes sickle-cell?

A

Glu6 is changed to Val in the beta chain mutation of Hb. The new Valine side chain can bind to a different Hb molecule to form a strand, which sickles the cell

77
Q

What is a prosthetic group?

A

Cofactor or coenzyme tightly (or covalently) attached to protein.

78
Q

What is a holoenzyme?

A

A catalytically active enzyme including all necessary subunits, prosthetic groups, and cofactors.

79
Q

What is an apoprotein?

A

Protein part of enzyme

80
Q

What are the 6 reactions of enzymes?

A

oxidoreductase, transferases, hydrolase, lyases, isomerases, and ligases

81
Q

What is a substate?

A

Molecule that is bound to the active site and is Acted upon by the enzyme.

82
Q

What is the transient state?

A

The transition state is the point where there is an equal probability of making the substrate or the products.

83
Q

What is the rate of the rxn dependent on?

A

[S]; [E] < [S]

84
Q

What does Km tell us?

A

Km establishes ~ cellular level of substrate.
Km associated with the affinity of enzyme for substrate
Km measures the likelihood of ES dissociating in either direction

85
Q

What is Kcat?

A

Kcat = Vmax/[Et] turnover number/rate constant; number of substrate molecules converted to product in a given unit of time when enzyme is saturated with substrate

86
Q

What is happening at the Vo?

A

[S] is much greater than the concentration of enzyme

87
Q

What is happening when Kcat< Km?

A

Km>Kcat = rapid turnover; high affinity for substrate

88
Q

How is the a-helix and beta -sheet stabilized?

A

The a-helix is stabilized by hydrogen bonds between nearby residues
The b-sheet is stabilized by hydrogen bonds between adjacent segments that may not be nearby

89
Q

What comprised a b-sheet?

A

multiple b-strands

90
Q

How are collagen fibers formed?

A

Collagen superstructures are formed by cross-linking of collagen triple-helices to form collagen fibrils.
Crosslinks are covalent bonds between Lys or HyLys, or His amino acid residues.

91
Q

How does Heme Binding to Protein Affect

CO vs. O2 Binding ?

A

The protein pocket decreases affinity for CO, but it still binds about 250 times better than oxygen.

92
Q

What is the difference in the curve of myoglobin and hemoglobin?

A

myoglobin - hyperbolic

hemoglobin - sigmoidal

93
Q

Explain Hb binding in the lungs and tissues

A

hemoglobin is more sensitive to the small differences in O2 concentration between the tissues and the lungs, allowing it to bind oxygen in the lungs (where pO2 is high) and release it in the tissues (where pO2 is low).

94
Q

How is the salt bridge formed?

A

His is protonated at lower pH forming the salt bridge with Asp favoring the T state
low pH = stabilize salt bridge = favored T state

95
Q

What are the properties of enzymes?

A

Catalytic (decreases activation energy, speeding up the rxn)
Allows for Specificity
Function in aqueous solutions under mild conditions

96
Q

What is the role of an enzyme?

A

Metabolites have many potential pathways of decomposition; Enzymes make the desired metabolic pathway the most favorable

97
Q

What are the assumptions of the Michaelis kinetics?

A

Concentration of enzyme is <

98
Q

What determines the fate of ES?

A

K-1 or K2

99
Q

What does the Kcat/Km ratio give us?

A

the efficient of an enzyme for a specific substate

100
Q

What is an inhibitor?

A

Inhibitors are compounds that decrease enzyme’s activity

101
Q

What is a irreversible inhibitor (inactivator)?

A

One inhibitor molecule can permanently shut off one enzyme molecule
They are often powerful toxins but also may be used as drugs

102
Q

What is a reversible inhibitor?

A

They are often structural analogs of substrates or products

They are often used as drugs to slow down a specific enzyme

103
Q

Where can reversible inhibitors bind?

A

to the free enzyme and prevent the binding of the substrate, or to the enzyme-substrate complex and prevent the reaction

104
Q

What happens during reversible uncompetitive inhibition?

A 
Only binds to ES complex 
-Does not affect substrate binding
-Inhibits catalytic function
Decrease in Vmax; apparent decrease in KM
No change in KM/Vmax
105
Q

What the difference between reversible uncompetitive and competitive inhibition?

A

Competitive - bind to the Same active site

Uncompetitive - binds at a Different site; line is parallel

106
Q

How does irreversible inhibition/suicide inactivators work?

A

Bind covalently with or destroy a functional group

107
Q

Strong vs. weak acid

A

a strong acid has greater tendency to lose its protons, higher Ka, and lower pKa than a weak acid

108
Q

What happens to if Km is high?

A

If Km high = k-1&raquo_space; k1 = weak affinity

If Km high = k2&raquo_space; k1 = product made

Biochemistry (4 decks)

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