Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Topics List E1 > Flashcards

Topics List E1 Flashcards

1
Q

polarity

A

results from uneven partial charge distribution btw various atoms in a compound.
e-‘s in these bonds are unequally shared btw the bond of a partially positive and partially negative atom.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

nonpolar

A

when molecules have atoms w/ = or nearly = electronegativities (small dipole moment)
or
it has polar bonds but molecular geometry is symmetrical. (dipoles cancel e/o out)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Bronsted-Lowry Acids

A

H+ donors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Bronsted-Lowry Bases

A

H+ acceptors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

H-bonds are a ____ force compared to a covalent bond.

A

weak

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

H-bonding forms?

A

the basis of a double-helix in vivo.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

In the peptide backbone of AA’s the H donors are the?

A

the H atoms attached to the O of the carbonyl or the H attached to the N of the amine group.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

In the peptide backbone of AA’s the H acceptors are the?

A

the more e-neg atoms, the O of the carboxyl group or the N of the amino group.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the first law of thermodynamics?

A

E is conserved, it cannot be created / destroyed, only converted from one form to another.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is Gibbs Free E?

A

a thermodynamic quantity = to the enthalpy (of a system / process) minus the product of entropy and the absolute temp.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

If dG is (+) then the rxn is?

A

nonspontaneous, an input of external E necessary for rxn to occur.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

If dG is (-) then the rxn is?

A

spontaneous, occurs w/o external E input.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

activation E

A

the min amount of E req’d to activate atoms / molecules to condition in which they can undergo a rxn.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

These can decrease the activation E req’d for a rxn to occur.

A

enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is a spontaneous rxn?

A

rxn that favors products at conditions under which rxn is occurring.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

equilibrium

A

chemical state when forward rate = reverse rate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Equilibrium is related to free E by?

A

Keq; equilibrium constant.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

If there’s no change in the reactants or products there’s no change in?

A

dG.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Keq

A

equilibrium constant, defines relative conc’s of products and substrates.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

If you ↑ [S] you ___ Keq?

A

decrease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

If you ↑ [P] you ___ Keq?

A

increase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

If there’s more reactants (substrates) the Keq is ___ and the denominator is ___?

A

Keq - smaller

denominator - larger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

If there’s more product the Keq is ___ and the numerator is?

A

Keq - larger

numerator - larger

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

For Gibbs free E if the denominator is ___ then ___ E is needed.

A

denominator larger

less E needed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

If there are less ___ it is ___ to move the rxn forward.

A

less products

easier to move rxn forward

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

A(n) ___ does not change the Free E (dG)

A

enzyme.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

rxn rate

A

A + B → C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

If the rxn rate is A + B → C and A is halved, the rate of the rxn will be?

A

halved.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Rxn rate depends on?

A

[products] and [reactants]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

pKa measures?

A

acid strength.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Ka

A

acid ionization constant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

How do you find the pKa?

A

-logKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

If the pKa is high it is less ___ and the proton dissociates ___ easily.

A

less acidic

proton dissociates less easily

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

If the pKa is low it is less ___ ?

A

less basic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

If the pH is low it’s more ___ and more likely to be ___.

A

pH low
more (+)
more likely to be protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

If the pH is high it’s more ___ and more likely to be ___.

A

pH high
more (-)
more likely to be deprotonated.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

How do you calculate pH?

A

-log[H+]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

buffer

A

chemical systems resistant to changes pH; help maintain neutral pH.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Henderson-Hasselbalch Eqn

A

calculates the pH of a buffer system.

pH = pKa +log [A-]/[HA]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

peptide bond

A

linkage btw 2 AA’s:
amide linkage btw carboxyl of AA and amino group of next AA. (recurring)
linear polymers of AA’s.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

When a peptide bond is formed a(n) ___ is removed to form a(n) ___ bond; therefore it is and example of ___.

A

water molecule
amide
dehydration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

A peptide bond is a(n) ___ linkage of ___ configuration.

A

covalent

trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

primary structure

A

seq of AA’s that make up a polypeptide chain.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

The primary structure of a protein (it’s AA sew) is important because it?

A

drives folding and intermolecular bonding of the linear amino chain which ultimately determines the proteins unique 3D shape.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

alpha helices

A

coiled structure of many proteins, consists of single chain of AA’s stabilized by H-bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

An alpha helix is a ___ structure.

A

secondary

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

A beta helix is a ___ structure?

A

secondary

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

beta sheets

A

parallel or antiparallel, form pleated sheets, R groups play a role.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is a parallel beta sheet?

A

C-terminus and N-terminus on same sides.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What is an antiparallel beta sheet?

A

C-terminus and N-terminus on each side.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What are some other structural components of secondary structures?

A

coiled coil, zinc finger, hairpin loops.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What are the 2 ends of a primary structure?

A
  1. Amino / N-terminus

2. Carboxy / C-terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

motifs

A

combinations of secondary structures, determined by appearance not function.

54
Q

domains

A

portion of protein that retains structure / function in absence of rest of protein, discretely folding 3D structure.

55
Q

helix-turn-helix is an example of a?

A

motif

56
Q

DNA-binding domain is an example of a?

A

domain

57
Q

Which way do we read primary structures?

A

Amino / N-terminus to Carboxy / C-terminus.

58
Q

The ___ structure is held together by H bonding.

A

secondary

59
Q

tertiary structure

A

gives overall 3-D shape of protein, combines elements of secondary structure, beta sheet and alpha helix.

60
Q

What are the stabilizing forces involved in protein structure?

A

van der Waals forces, H-bonds, disulfide bridges, salt bridges.

61
Q

monomers

A

single chains of AA’s folded into active protein.

62
Q

___ can be subunits of multimers

A

monomers

63
Q

multimers

A

several subunits, each has its own protein monomer (polypeptide chain), each labeled based on function (catalytic, regulatory, etc.), not covalently linked.

64
Q

Dimers, trimers, and tetramers are examples of?

A

multimers

65
Q

Somatic hypermutation (SHM)

A

occurs in differentiation B cells and enables even more variety in the Fab domains of Ab’s.

66
Q

 ACE-binding residues

A

AA mutations

67
Q

“Sustainer” patients

A

↑ anti-SARS-CoV19 immunity over successive draws.

68
Q

“Decayer” patients

A

↓ immunity along w/ ↓ Igs

69
Q

What can modify / change an AA?

A

Change in pH, phosphorylation, disulfide bond, and a mutation of the genome

70
Q

disulfide bonds

A

play key role in stabilizing protein structures, disruption strongly associated w/ loss of protein function and activity

71
Q

Enzyme: hexokinase

A

1st enzyme that functions in glycolysis

72
Q

Enzyme: phosphatase

A

removes a phosphate

73
Q

Enzyme: lactase

A

breaks down lactose

74
Q

Enzyme: sucrase

A

breaks down glucose

75
Q

-ase

A

enzyme

76
Q

Enzymes stabilize the ___ by donating e-‘s that the enzyme will eventually recover.

A

transition state

77
Q

Enzymes are also called?

A

catalysts

78
Q

Enzyme: chymotrypsin

A

digestive enzyme

79
Q

Enzyme: protease

A

degrades proteins

80
Q

Enzyme: ACE2

A

human enzyme, helps virus infect us

81
Q

Enzymes increase ___ , decrease ___, and don’t effect ___.

A

increase rate of rxn
decrease activation E,
don’t effect dG.

82
Q

fusion protein

A

protein made from fusion gene, created by joining parts of 2 diff genes.
At least 2 domains.

83
Q

Functions of fusion proteins?

A
  1. aids in cloned gene purification
  2. report expression level
  3. histochemical tags to visualize location of proteins.
84
Q

epitope tags

A

biological structure / seq (protein / carbohydrate) that acts as an antigen which is recognized by an antibody.

85
Q

Functions of epitope tagging?

A
  1. detect proteins when no Ab is available.
  2. characterize newly discovered proteins / low abundant proteins.
  3. can id / purify favorite protein
86
Q

Protein Purification: Salting Out

A

a lot of salt makes charged molecules precipitate

87
Q

What are the Column-based methods of protein purification?

A
  1. Size-exclusion chromatography
  2. ion-exchange chromatography
  3. affinity chromatography
88
Q

Protein Purification: Size-Exclusion Chromatography

A

separates proteins based on size.

89
Q

In Size-Exclusion Chromatography the ___ proteins reside longer in beads and the ___ proteins elute in early fractions.

A

small reside longer.

large elute early

90
Q

The gel beads in Size-Exclusion Chromatography have pores that?

A

allow smaller molecules to enter and excludes molecules larger than the pores.

91
Q

Protein Purification: Ion Exchange Chromatography

A

separates proteins based on charge.

92
Q

In Ion-Exchange Chromatography the stationary phase is?

A

charged, binds proteins w/ opp charge.

93
Q

In Ion-Exchange Chromatography you can elute using?

A

salt, pH change.

94
Q

Protein Purification: Affinity Chromatography

A

isolates specific proteins by taking advantage of specific interactions btw protein and stationary phase.

95
Q

The stationary phase of Affinity Chromatography can be loaded with?

A

ligand / Ab / epitope tags

96
Q

Protein Purification: Immunoprecipitation

A

uses Ab’s, Ig Fc linked beads which work like stationary phase in a column.
Ab’s heavy, separate using centrifuge.

97
Q 
Which of the following won’t affect your antibody’s binding to a target protein?
A.
Change in the epitope
B.
Change in the pH
C.
Change in the Fab
D.
Change in the Fc
E.
All of the above will affect your antibody’s affinity for the target it usually recognizes.
A

D. Change in the Fc

98
Q

All chromatography techniques involve movement of a compound with a ___ over a ___?

A

mobile phase over a stationary phase.

99
Q

Yield is equivalent to?

A

total amount protein (activity) in final sample / amount protein (activity) in crude sample

100
Q

Fold Purification equivalent to?

A

specific activity in final sample / specific activity in crude lysate

101
Q

Suicide Inhibitors

A

directly poison enzyme

covalently modify enzyme active site, irreversible block function.

102
Q

A pesticide is an example of a?

A

suicide inhibitor

103
Q

The only type of irreversible inhibitor is?

A

suicide inhibitors

104
Q

What are the 3 types of reversible inhibitors?

A

Competitive
Uncompetitive
Noncompetitive

105
Q

Competitive Inhibition

A

recognizes molecules similar to shape of substrate that binds to active site.
competes w/ substrate
can overcome by increasing substrate.

106
Q

Competitive Inhibitors increase ___ but do not change the ___.

A

increase Km

don’t change Vmax

107
Q

Competitive inhibitors will do what on a double reciprocal graph?

A

intersect with the line where no inhibitor is present.

108
Q

Uncompetitive inhibitors will do what on a double reciprocal graph?

A

will not intersect with the line where no inhibitor is present.

109
Q

Uncompetitive Inhibitors decrease both ___ and ___.

A

Km and Vmax

110
Q

Uncompetitive inhibitors bind the ___.

A

{ES] complex

111
Q

Uncompetitive requires ____?

A

substrate.

112
Q

Noncompetitive Inhibition has no change in ___ but decreases ___.

A

no change in Km
decreases Vmax
Increasing [S] doesn’t alleviate inhibition.

113
Q

In Noncompetitive Inhibition the ___ and ___ bind at different sites

A

substrate and inhibitor

114
Q

Noncompetitive Inhibition will do what on a double reciprocal graph?

A

only intersect on the x-axis, at the very beginning of the line on the (-) side of the y-axis.

115
Q

Protein: aquaporin

A

transmembrane protein.
Acts as pore / channel in membrane, extends above / below plasma membrane.
Selectively allows water passage in / out of cell.

116
Q

Aquaporin has a(n) ___ interior and a(n) ___ exterior

A

hydrophilic interior

hydrophobic exterior

117
Q

Water diffusion in aquaporin is controlled via?

A
  1. Gating: controlled by phosphorylation / ionization of R groups.
  2. Trafficking: response to environmental osmolarity changes (rain)
118
Q

Protein: chymotypsin

A

Digestive enzyme
Cleaves dietary proteins into peptides
Contains active site and regulatory site.

119
Q

The composition of chymotrypsin is?

A

2 beta barrels

1 short alpha helix.

120
Q

Structure of chymotrypsin

A

Protease: enzyme that degrades proteins.
3 polypeptides linked by S-S.
Starts as inactive precursor, trypsin then cleaves off inhibitory domain to activate it.

121
Q

Protein: Collagen

A

structural protein

Fibrous protein, concentrated in muscle, connective tissue.

122
Q

Composition of Collagen

A

Composed of triple helix:
Glycine (33%)
Proline (16%)
Hydroxyproline (16%)

123
Q

Protein: Antibodies / Immunoglobulins (Ig)

A

binding proteins

Large proteins made by immune system that recognize, bind to antigens.

124
Q

Function of Antibodies / Immunoglobulins (Ig)

A

Detect foreign bacteria / viruses.

Mark for engulfment by phagocytic cells (destruction).

125
Q

Structure of Antibodies / Immunoglobulins (Ig)

A

Y

126
Q

Solid-Phase Peptide Synthesis (SPPS)

A

best for small peptides doesn’t include protein chaperones
modifying enzymes
cellular cond’s hard to replicate in test tube system.

127
Q

Why use protein overexpression instead of SPPS?

A

larger size range, benefits of other cell components.

128
Q

lysosome

A

membrane-bound organelle, contains digestive enzymes, break down excess / worn-out cell parts.

129
Q

Protein: Src

A

non-receptor tyrosine kinase encoded by SRC gene.

transduces signals involved in control of cellular processes (proliferation, differentiation, motility / adhesion)

130
Q

carbonic anhydrase

A

in RBC
Aids in conversion of CO2 to carbonic acid and bicarbonate ions.
Converts bicarbonate ions back to CO2 (breathe out).

131
Q

ATCase

A

catalyzes committed step in pathway that ultimately yields pyrimidine nucleotides such as cytidine triphosphate (CTP).

132
Q

spike protein

A

glycoprotein

allows coronaviruses to enter cells

Biochemistry (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions