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Biochem midterm 2 > Midterm 1 > Flashcards

Midterm 1 Flashcards

(102 cards)

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1
Q

What is a covalent bond?

A

2 atoms sharing a pair of electrons, a really tight bond

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2
Q

What is a hydrogen bond?

A

Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a covalently bound hydrogen and a lone pair of electrons

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3
Q

Water is a good solvent for what type of molecules?

A

charged and polar
- amino acids and peptides
small alcohols
carbohydrates

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4
Q

Water is a poor solvent for what type of molecules?

A

nonpolar substances.
nonpolar gases
aromatic moieties
aliphatic chains

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5
Q

What is an ionic interaction?

A

electrostatic attraction between oppositely charged ions.

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6
Q

What is a hydrophobic interaction?

A

interaction between hydrophobic compounds and water.

hydrophobic compounds tend to cluster together to increase entropy

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7
Q

What are Van der waals interactions?

A

weak interaction between two atoms depending on their distance from each other.

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8
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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9
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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10
Q

Describe water adhesion

A

binding between water and something else (plastic or glass). menisque.

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11
Q

Describe water cohesion:

A

binding between water and water by hydrogen bonds, surface tension.

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12
Q

Describe proton hopping

A

proton moving along a chain of covalent and hydrogen bonds interchangeable in water.

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13
Q

What is the formula for pH?

A

pH= -log[H+]

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14
Q

What is the formula for the equilibrium constant?

A

concentration of product/concentration of reactants.

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15
Q

What is a conjugate acid?

A

a substance that gained a proton

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16
Q

What is a conjugate base?

A

a substance that lost a proton.

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17
Q

What is the difference between a strong acid and a weak acid?

A

A strong acid will more easily lose its proton than a weak acid.

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18
Q

Give the formula for pka

A

pka=-logKa

ka=keq

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19
Q

What is the relationship between a strong acid and its pka?

A

stronger the acid, lower its pka

high pka= weak acid

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20
Q

What is a buffer system?

A

weak acid and conjugate base that resists change in pH when acid or base are added.

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21
Q

When is the greatest buffering capacity of a system?

A

when ph=pka

there is a 50:50 mixture of acid and anion forms of the compounds

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22
Q

When is the buffering capacity of a system lost?

A

when the pH differs from pka by more than 1 pH unit

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23
Q

Give the handerson-hasselbach equation

A

ph=pka+ log [conjugates base]/[weak acid]

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24
Q

What are the biological functions of proteins?

A

catalysis
transport
structure
motion

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25
Describe the formation of a peptide bond
condensation reactions of 2 amino acids put together.
26
Name the 4 groups in amino acids
H group Carboxyl group Amino group R group
27
What are the particularities of aromatic amino acids?
possess a cyclic group
28
What is the only amino acid that is not chiral?
glycine
29
What is the particularity of cysteine?
can form disulfide bonds
30
Why is proline unique?
the R group is cyclical (non polar)
31
What are the two amino acids containing sulphur atoms?
methionine and cysteine
32
What is the function of reversible modifications of amino acids?
increase or decrease a protein activity.
33
What is the charge of an amino acid with a neutral R group at low pH?
positive
34
what is the charge of an amino acid with a neutral R group at high pH?
negative.
35
What is a zwitterion?
single-molecule has both a positive and negative charge
36
How do you calculate the isoelectric point?
average between the two pka concerned for the formation of that molecule.
37
What forces are stabilizing protein structure?
non-covalent forces | (ionic, hydrophobic, van der Waals, disulphide, hydrogen bond
38
Why are disordered regions important in proteins?
for interactions with other proteins.
39
What is a resonance hybrid?
the double bond can move from the C=O to C=N
40
what is the phi angle?
the angle between the Carbon-N bond
41
what is the psi angle?
the angle between the Carbon-Carbonyl bond
42
What are the two regular arrangements in the secondary structure of proteins?
alpha helix | et beta-sheets
43
What amino acids are considered helix breakers?
proline and glycine | stretches of bulky or charged amino acids
44
Where would we find the negatively charged residues in a helix?
near the positive end (amino terminus)
45
Where would we find the positively charged residues in a helix?
near the negative end (carboxyl terminus)
46
What residues are preferred in beta sheets?
large aromatic or branched residues
47
What amino acids are more likely to be found in b turns?
proline (position 2) and glycine. (position 3)
48
What interactions stabilize the tertiary structure?
numerous weak interactions
49
What characterizes a fibrous protein?
insoluble | consist of a single type of secondary structure
50
What characterizes a globular protein?
often contains several types of secondary structures
51
What is a protein domain?
part of a polypeptide chain that is independently stable or could undergo movements as a single entity.
52
Name 4 fibrous proteins?
alpha-keratin myosin collagen silk fibroin
53
What makes silk fibroin so flexible?
sheets are held together by numerous weak interactions.
54
What are the advantages of the quaternary structure of proteins?
accumulates a greater number of weakly stabilizing interactions. gain in stability relative reduction in exposed surface improves catalysis or tight regulation slower though.
55
What type of protein are the enzymes mostly?
globular
56
What is a prosthetic group?
cofactor tightly bound to protein
57
What is an apoenzyme?
enzyme without cofactor
58
What is a holoenzyme?
enzyme with coenzyme
59
What is an organic cofactor?
coenzyme
60
What is the function of oxidoreductases?
enzyme that catalyzes the transfer of electrons
61
What is the function of a transferase?
enzyme that catalyzes a group transfer reaction
62
What is the function of a hydrolase?
enzyme that catalyzes hydrolysis (transfer of functional groups to water)
63
What is the function of a lyase?
cleavage of C-C, C-O, C-N or other bonds by elimination, leaving double bonds or rings or adding groups to double bonds.
64
What is the function of an isomerase?
transfer of groups within molecules to yield isomeric forms.
65
What is the function of ligase?
formation of C-C, C-S, C-O and C-B bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
66
How do the enzymes accelerate reactions?
decrease the activation energy
67
What allows the enzyme to decrease considerably the activation energy?
enzyme specificity, | transition state, conformational change.
68
What are the three catalytic mechanisms of enzymes?
acid-base catalysis covalent catalysis metal ion catalysis
69
What is the principle of acid-base catalysis?
give and take protons
70
What is the principle of covalent catalysis?
a transient covalent bond between the enzyme and the substrate.
71
What is the principle of metal ion catalysis?
involves a metal ion bound to the enzyme. stabilizes negative charges.
72
What two-step reaction is catalyzed by chymotrypsin?
acylation (fast) | deacylation (slow)
73
At what pH does chymotrypsin work better?
basic pH.
74
What are the two catalysis mechanisms involved in the peptide cut by chymotrypsin?
base catalysis | covalent catalysis
75
What is the principle behind column chromatography?
proteins with a lower affinity for the solid phase will wash off first. protein with higher affinity will retain on the column longer
76
What is the principle of ion exchange chromatography?
protein migrates through the column according to its physical-chemical (charge) properties
77
what is the principle of size exclusion chromatography?
larger proteins migrate first, small proteins enter numerous pores and take a longer path.
78
What is the principle of affinity chromatography?
protein can bind to a ligand, antibody, or other proteins. purification depends on the affinity of interaction (or affinity of binding)
79
What is the principle of electrophoresis?
the electric field pulls protein according to their charge
80
What does SDS do in SDS PAGE?
gives all proteins a uniformly negative charge | denaturing.
81
What is the function of SDS page?
analyze proteins based on their molecular weight
82
What is the difference between SDS page, non-reducing SDS page and native page?
SDS page: denature and gives a negative charge. + break of disulfide bond non-reducing: only negative charge, not breaking the disulfide bond native: no detergent. no denaturation. slight charge only
83
What is the function of isoelectric focusing?
can be used to determine the pI of a protein
84
What is 2D electrophoresis?
separate proteins by pI and by molecular weight. | SDS-PAGE+ isoelectric focusing
85
What is the maximum velocity?
when the reaction reaches a plateau
86
What is the Michaelis Menten constant?
the concentration of substrate providing half of the enzyme maximal velocity. km
87
Describe the saturation kinetics?
at high substrate concentration, velocity is not proportional to [S]
88
What is the Michaelis-Menten equation?
V0=Vmax[S]/Km+[S]
89
Give the definition and the equation for the turnover number?
Kcat=Vmax/[ET] | Kcat= number of S molecules converted to P per time.
90
What is the equation for enzyme efficiency?
Kcat/Km
91
What gives you the slope value in the Lineweaver-Burk plot?
Km/Vmax
92
What gives you the y-intercept in the Lineweaver-Burk plot?
1/Vmax
93
What gives you the x-intercept in the Lineweaver-Burk plot?
-1/Km
94
What is the function of inhibitors?
compounds that decrease an enzyme's activity
95
What is competitive inhibition?
competes with the substrate for binding. binds active site. does not affect catalysis. - no change in Vmax, increase in Km lines intersect at the y axis
96
What is uncompetitive inhibition?
only bind to Enzyme-substrate complex. does not affect substrate binding. inhibits catalytic function. decrease in V max, an apparent decrease in Km. parallel lines
97
What is mixed inhibition or non-competitive inhibition?
binds enzyme with or without substrate to inhibit both substrate binding and catalysis. decrease v max, the apparent change in km. lines intersect left from the y-axis. or start from the same point and diverge.
98
Define irreversible inhibitors
react with the enzyme. one inhibitor molecule can permanently shut off one enzyme molecule. powerful toxins.
99
Name the 4 processes by which an enzyme can be regulated?
- noncovalent modification - covalent modification - irreversible - reversible
100
What are allosteric effectors?
noncovalent modification. | can improved or reduce enzymatic catalysis
101
What covalent modifications can regulate protein activity?
phosphorylation adenylation acetylation myristoylation.
102
What are zymogens?
proenzyme inactive precursor of an enzyme. irreversible covalent modification can activate zymogens

Biochem midterm 2 (3 decks)

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