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Biochem Weeks 1-2 > protein structure > Flashcards

protein structure Flashcards

1
Q

pH =

A

-log of hydrogen ion concentration

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2
Q

in a neutral solution … and …

A

pH is 7.0

concentration of H ions = concentration of OH ions

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3
Q

strong acids dissolve / dissociate … in water

A

completely

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4
Q

weak acids dissolve / dissociate … in water

A

only partially

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5
Q

an acid’s extent of dissociation in water is determined by …

A

the acid dissociation constant Ka

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6
Q

lower pKa =

A

stronger acid

(or more likely it is to donate protons)

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7
Q

a buffer is …

A

a system consisting of a weak acid and its anion (aka salt, or conjugate base)

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8
Q

the best buffering capacity for H+ and OH occurs at …

A

pH = pKa

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9
Q

weak acids are important because they can function as …

A

buffers

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10
Q

most drugs are …

A

weak acids / bases

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11
Q

amino acids with positive charged side chains

A

arginine

histidine

lysine

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12
Q

amino acids with negative charged side chains

A

aspartate (aspartic acid)

glutamate (glutamic acid)

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13
Q

amino acids with polar uncharged side chains

A

serine

threonine

asparagine

glutamine

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14
Q

special cases of amino acids (may not need to know)

A

cysteine

selenocysteine

glycine

proline

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14
Q

amino acids with hydrophobic side chains

A

alanine

valine

isoleucine

leucine

methionine

phenylalanine

tyrosine

tryptophan

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15
Q

synthesis of an amino acid occurs … to … end

A

N (amino) terminal to C (carboxyl) terminal

16
Q

glycine’s R group is … making it …

A

just -H

making it very small, maximizing flexibility / ability to rotate when in polypeptide chain

17
Q

proline links … to …, which causes … in a polypeptide chain

A

the alpha carbon to the amino nitrogen

rigidity when in a polypeptide bc rotation of the polypeptide is very limited/impossible at those bonds

18
Q

structure / shape determines …

A

function

19
Q

tertiary structure of proteins have two major classes:

A

fibrous and globular (water or lipid soluble)

20
Q

a disordered region of a protein is …

A

a region that is flexible and may be stabilized after binding to another factor

flexibility in shape = flexibility in function

21
Q

chaperone proteins assist in …

A

protein folding by binding to and stabilizing hydrophobic regions

ex. HSPs (heat shock proteins)

22
Q

non-covalent interactions within proteins that contribute to its shape / structure:

A

ionic interactions

dipole interactions

hydrophobic effect

van der Waals interactions (weak, temporary dipole/steric repulsion)

23
Q

tertiary protein structure can be stabilized by …

A

cysteine, bc it forms covalent disulfide bonds

24
Q

protein denaturation means …, and can occur by …

A

unfolding of a protein, which means loss of function / activity bc there is a loss of shape

heat / cold
pH extremes
organic solvents
chaotropic agents

25
Q

cofactor vs prosthetic group

A

cofactor- is necessary for function

prosthetic group- is bound tightly

26
Q

K on and K off are …

A

K on = rate constant for forward rxn

K off = rate constant for reverse rxn

27
Q

the equilibrium dissociation constant, Kd, describes …

A

the affinity of a protein for its ligand

LOW Kd = higher [PL]
therefore tighter binding of P + L

28
Q

in a graphical representation of ligand binding, theta is …

A

the fraction of ligand-binding sites that are occupied

y-axis

29
Q

in a graphical representation of ligand binding, theta (fraction of occupied ligand-binding sites) is plotted against …, and the curve represents …

A

the concentration of free ligand [L]
x-axis

a binding curve for ligand L

30
Q

in a graphical representation of ligand binding, then Kd is equivalent to …

A

the [L] at which 1/2 of the available ligand-binding sites are occupied

31
Q

in a graphical representation of ligand binding, the equation for theta is …

A

theta = [L] / [L] + Kd

Biochem Weeks 1-2 (8 decks)

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