Brainscape's Knowledge GenomeTM

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


See full index

Biochemistry 450 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

Covalent bonds

A

Very strong bonds that hold molecules together. Glue for bio molecules

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

Hydrogen bonds

A

very important in stabilizing protein and DNA structures. Much weaker bonds. Uneven sharing of electrons between N- H or O-H

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

Why does water have relatively high boiling point?

A

Due to numerous hydrogen bonds.

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

DNA double helix is held together by

A

hydrogen bonds between individual bases

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

When are Hydrogen bonds the strongest?

A

They provide greater stability in numbers. Less stability locally (easily pull them apart when DNA needs to be replicated)

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

What disrupts protein structure/denatures proteins?

A

Disruption of Hydrogen bonds

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

pH measures

A

measure of the proton concentration in a solution

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

The lower the pH…

A

the higher the hydrogen ion concentration and the stronger the acid.

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

pH + pOH =

A

14

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

pOH =

A

-log[OH-]

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

pH =

A

-log [H+]

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

pKa =
what is pKa?
what is Ka?

A

-log[Ka]
pKa is the strength of an acid
Ka is the acid dissociation constant

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

The lower the pKa for an acid system

A

the stronger the acid is

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

Acetic acid (HAc)

A

a weak acid, it does not completely dissolve in water.

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

HCl

A

a strong acid, completely dissociates in water. Strong acids do not have pKa or Ka values

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

Weak Acid

A

Molecule containing the most protons in a weak acid system (HA)

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

Henderson-Hasselbalch

A

States: pH = pKa + log {[A-]/[HA]}

where [A-] is the concentration of salt and [HA] is the concentration of acid.

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

Gain or loss of a proton-

A

causes molecule to gain or lose one full charge.

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

Carboxylic Acid system’s two forms:

A

COOH (acid) and COO- (salt)

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

Weak Acid dissociation

A

HA, dissociate in water to a limited extent. Ionization is written as HA H+ + A-
(where H+ is the weak acid and A- is the salt - lost a proton)
The Henderson-Hasselbalch equation applies.

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

Amine systems have two forms:

A

NH3+ (acid) and NH2 (salt)

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

Buffer definition

A

A solution that resists change in pH.

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

When is buffer system at maximum capacity?

A

When concentration of HA equals concentration of Ac- (Weak Acid = Salt) This is also where pH = pKa according to the Henderson Hasselbalch equation (log of 1 is zero)

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

Buffer system example

A

HAC/Ac- system acts as a buffer because Ac- gobbles up protons when added and HAc releases protons when protons are removed by NaOH.

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

Addition of Protons (ex: HCl - strong acid) will drive HA H+ + Ac- system to which side?

A

The left. This will increase HA and decrease Ac-. Salt in converted into acid

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

Removing protons (ex: NaOH - strong base) will drive HA H+ + Ac- system to which side?

A

Right. This will decrease HA and increase Ac-. Acid converted into salt.

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

In a systems buffering range- For every molecule of HCl added, what happens to A- and HA. What if you had 500 molecules of each and added 10 molecules of HCl?

A

one molecule of A- is converted to HA. You would have 510 HA and 490 A- molecules.

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

In a systems buffering range- For every molecule of NaOH added, what happens to A- and HA. What if you had 500 molecules of each and added 10 molecules of NaOH?

A

one molecule of HA is converted into A-. You would have a solution of 510 molecules of A- and 490 molecules of HA.

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

What allows the system to be in its buffering range?

A

pH must be less than one unit above or below pKa.

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

When are buffers maximally effective?

A

When pH = pKa. It is reasonably effective if its within one pH unit above or below.

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

Loss or gain of protons in amino acid groups causes

A

change in charge from zero to +1 or zero to -1

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

Amino acid charge changes affect…

A

its interactions with neighboring amino acids and proteins. Changes in attraction/repulsion.

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

Henderson Hasselbalch equation allows to

A

predict the ratio of salt to acid as a function of pH if pKa is known.

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

Small pH changes

A

make a big difference in body

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

The log of a number less than one =

A

a negative number (implying that there is more [acid] than [salt])

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

How many buffering regions does alanine have?

A

Two regions because it has an amine group and a carboxyl group which allows it to have two pKas/ two regions where it can gain/lose electrons.

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

If pH is more than one unit above the pKa of a group, the proton is…

A

ON it.

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

If pH is more than one unit below the pKa of a group, the proton is…

A

OFF it.

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

pI =

A

the average of the pKa values on either side of the location on the titration plot where the zero-charged molecule is found. The pH where molecule has zero charge.

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

Can the pI be estimated?

A

No it must be calculated.

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

Protein structure dictates-

A

Protein function.

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

Structure of the protein is a function of

A

the sequence of amino acids comprising it.

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

Amino acids

A

monomeric units of proteins covalently joined together by peptide bonds to make proteins (polypeptides).

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

Aliphatics

A

Glycine, Alanine, Proline, Valine, Leucine

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

How many amino acids? How many are chiral? Which is/are not?

A

20 amino acids
19 are chiral
Glycine is achiral

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

Almost all biologically made amino acids are in what stereoisometric form?

A

L- form

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

Where does D form of a protein occur?

A

Occurs rarely, such as in cell wall of bacteria.

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

5 groups of amino acids:

A

Aliphatics, Hydrophobics, Polar, Positive R-groups, Negative R-groups

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

Hydrophobics

A

Isoleucine, Methionine, Tryptophan, Phenylalanine

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

Polar

A

Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine (sulfhydral group that can ionize)

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

Positive R groups

A

Lysine, Arginine, Histidine

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

Negative R-groups

A

Aspartate, Glutamate (aspartic acid and glutamic acid)

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

Ionizable groups:

A

Aminos, Carboxyls, sulfhydryl part of cysteine, histidine, aspartic/glutamic acid, tyrosine, lysine, argenine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is the most simple amino acid? Why?

A

Glycine because it only has a hydrogen as its R group and is the only amino acid to not have D- or L- forms.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is interesting about proline?

A

The amino group is a ring and it is therefore very inflexible.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

Primary Structure-

A

The sequence of amino acids.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

Peptide bond

A

Bond holding amino acids together which occur between the alpha amino group and the alpha carboxyl group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

How do peptide bonds behave?

A

They form resonance structures and behave like double bonds. Double bonds can’t rotate and therefore define a plane.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

How are alpha carbons on either side of a peptide bond generally arranged? Which amino acid is the exception?

A

In the trans configuration (10,000 trans to 1 cis). When proline is involved then trans configuration is only favored 100 to 1.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

How do the bonds around alpha carbon behave?

A

They can both rotate because they are single bonds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

How can you describe a polypeptide?

A

A series of planes separated by an alpha carbon, with each plane being rotated a certain number of degrees relative to the alpha carbon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Phi angle -

A

rotational angle around the single bond between the alpha amino group and the alpha carbon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Psi angle-

A

rotational angle around the single bond between the alpha carbon and the alpha carboxyl.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

Ramachandran Plot

A

plot of theoretical rotations of psi vs. phi and calculates which of these angle would prove stable structures.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

Secondary structure (examples)

A

regular/repeating structure arising from interactions between amino acids that are close (less than 10 amino acids away).
Ex: alpha helices, beta strands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

Tertiary structure

A

Interactions between amino acids that are more than 10 amino acids away.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

Secondary structure is stabilized by

A

hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

How do alpha helices form?

A

a carbonyl oxygen from a peptide bond forms a hydrogen bond with an amine nitrogen of another peptide bond four amino acids away.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What amino acids are favorable for alpha helices? Which are not?

A

Favorable: amino acids with simple side chains- alanine
Unfavorable: bulky or cyclic side chains- tryptophan or proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

How do Beta strands form? What amino acid favors disruption?

A

consist of amino acid backbones in a V shape –like pleats of a drape– Helix in two dimensions. Proline favors disruption.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

How do beta sheets arise?

A

arise from the arrangement of beta strands. Hydrogen bonds between beta strands (parallel/antiparallel) so that the carbonyl oxygen of one side interacts with the amine hydrogen of the other.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

What can beta strands do regarding their orientation?

A

The can orient their R groups such that they interact appropriately (hydrophobic-hydrophobic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What is an essential feature of proteins for overall structure?

A

Turns/Bends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

What do turns do to secondary structure?

A

They often interrupt secondary structure (alpha helices/beta strands) and involve proline/glycine residues.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

Collagen

What does it contain?

A

Another fibrous protein that is the most abundant in your body. Contains intertwined helices comprised of abundant repeating units of glycine, proline, and hydroxylproline.

76
Q

What makes collagen so sturdy?

A

Hydroxyls of hydroxyprolines can react with one another and form covalent cross-links.

77
Q

Hydroxylation of proline

A

It is a post-translational modification (after protein is made) and hydroxyls are placed there in a reaction involving vitamin C.

78
Q

What does vitamin C deficiency cause?

A

scurvy (very weak collagen)

79
Q

Zwitterion

A

molecule/compound that has an overall net charge of zero.

80
Q

Tertiary structure

A

Interactions between amino acids that are more than 10 amino acids away. Possible by folding protein chain to brings distant amino acids closer together.

81
Q

What is tertiary structure stabilized by?

A

Disulfide bonds, ionic interactions, hydrogen bonds, metallic bonds, and hydrophobic interactions.

82
Q

Disulfide bonds-

A

strongest forces holding tertiary structure together, since they are covalent.

83
Q

Most proteins are what shape in nature? How does this arise

A

They are globular which arises from folding, which allows them to have proper shape and function.

84
Q

Instructions for folding protein are in

A

contained in amino acid sequence.

85
Q

Levinthal’s paradox

A

folding is not a random event, but rather based on an ordered sequence of events arising from the chemistry of each group.

86
Q

Myoglobin

A

Protein that acts as an oxygen battery, storing oxygen in muscles. Contains a heme group that contains iron.

87
Q

Prosthetic group- definition and example

A

refers to a non- amino acid containing group that binds to a protein and augments its function. Example: heme group

88
Q

How are amino acids in myoglobin arranged?

A

hydrophilic and ionic amino acids are arranged on outside and hydrophobic amino acids are largely arrangle on the inside.

89
Q

How are amino acids in myoglobin arranged?

A

hydrophilic and ionic amino acids are arranged on outside and hydrophobic amino acids are largely arrange on the inside.

90
Q

What do membrane proteins usually have?

A

they have external amino acids that are hydrophobic so they can interact with nonpolar membrane.

91
Q

Porin

A

Membrane protein that has a hole in the center that allows water to pass through it. Nonpolar amino acids are on the outside and polar amino acids are on the inside.

92
Q

Quaternary Structure

A

interactions between separate polypeptide chains within the protein. A protein can contain one or more polypeptides and may be covalently modified.

93
Q

Example of quaternary structure

A

hemoglobin- has multiple subunits. Interactions between the subunits include ionic interactions, hydrogen bonds, and hydrophobic interactions.

94
Q

Ribonuclease (RNase)

A

enzyme that is very stable to heat and other things that denature/inactivate other proteins. Disulfide bonds help it to remain resistant to denaturation.

95
Q

How can disulfide bonds of RNase be broken?

A

they can be denatured with a reagent like mercaptoethanol followed by heating it to 100 degrees Celsius. Causes loss of activity.

96
Q

What does removal of mercaptoethanol and urea from a solution do to RNase?

A

it allows RNase to refold and establish the correct disulfide bonds. This shows that primary sequence is driving force for protein folding.

97
Q

Chemicals that can disrupt forces hold tertiary and quaternary structure:

A

Urea, guanidinium chloride (disrupts hydrogen bonds), ptotons (ionic bonds), detergents (hydrogen bonds), dithiothreitol (DTT) can break disulfide bonds and make sulfhydryls.

98
Q

Levinthal’s paradox

A

folding is not a random event, but rather based on an ordered sequence of events arising from the chemistry of each group. If it were random, not enough computational power to figure out what causes the folding.

99
Q

Tendency of amino acids to participate in alpha helices, beta strands/sheets, and turns helps us predict what structure?

A

Secondary structure, but not tertiary structure.

100
Q

Prions

A

infectious misfolded proteins implicated in diseases

101
Q

Example of disease/diseases with prions

A

Mad cow disease and Creutzfeld-Jacob disease are brain-wasting disease that results in misfolding of a brain protein known as PrP. misfolded protein converts other proteins to misfolded state also.

102
Q

Chaperons/Chaperonins:

Induced by?

A

provide mechanism to insure proteins fold properly. They are induced by heat shock of cells.

103
Q

Protein purification

A

exploits difference in charge, size, shape, and affinity for specific compounds.

104
Q

Centrifugation/artificial gravity

A

Separates protein according to size. Precipitates cellular components. The faster the rotor spins, the smaller the compound/structure one can precipitate.

105
Q

zonal centrifugation

A

used simple to separate molecules, not precipitate them.

106
Q

Dialysis

A

Allows to separate large molecules (protein/DNA) from tiny molecules/salt but not isolate the protein. Encases the protein/salt mixture in a membrane which has pores that the small molecules leak out of.

107
Q

Gel filtration/gel exclusion chromatography

A

Separates large and small molecules by using beads with tunnels/holes in them of fixed size (exclusion limit). Beads are packed into column and smaller molecules can enter the beads and come out last.

108
Q

Ion exchange chromatography

A

Separates by charge. Beads in a tunnel have a certain charge (positive or negative) and molecules of the opposite charge stick to the beads and come out last.

109
Q

Affinity chromatography

A

relies on the tendency of many proteins to bind to molecules.

110
Q

Affinity chromatography

A

relies on the tendency of many proteins to bind to molecules. Uses beads in a tunnel, but coats beads with a certain molecule, such as ATP. Proteins which bind to the molecule will stick to the bead and come out last.

111
Q

Gel Electrophoresis

A

Uses electrical current to separate molecules according to size (DNA or protein). DNA is negative charged (because of phosphate backbone) and repel away from negative electrode.Their speed is a function of size so smaller ones move farther.

112
Q

Two gels in gel electrophoresis

A

Agarose gels used to separate DNAs and polyacrylamide used to separate proteins.

113
Q

Gel Electrophoresis

A

Uses electrical current to separate molecules according to size (DNA or protein). DNA is negative charged (because of phosphate backbone) and repel away from negative electrode (top) and go towards positive (bottom).Their speed is a function of size so smaller ones move farther.

114
Q

PolyAcrylamide Gel Electrophoresis (PAGE)

A

Separates molecules on basis of size, with strands of polyacrylamide as the gel (it is meshlike). More polyacrylamide crosslinked= harder for molecules to pass. Uses SDS as a coat if using proteins.

115
Q

SDS-PAGE

A

Used to separate proteins by size, which are globular and can be negative, positive, or neutral in their native state. Detergent sodium dodecyl sulfate (SDS) added to proteins, which denature and become (-) charged rods like DNA.

116
Q

Techniques for breaking polypeptides into pieces (polypeptide cleavage agents):

A

Cyanogen bromide, trypsin, chymotrypsin, thrombin, carboxypeptidase.

117
Q

Cyanogen bromide

A

chemical that cleaves carboxyl side of methionines

118
Q

trypsin

A

an enzyme that cleaves on carboxyl sides of lysine and argenine

119
Q

chymotrypsin

A

enzyme that cleaves on carboxyl side of tyrosine, tryptophan, phenylalanine, leucine, and methionine

120
Q

thrombin

A

cuts on the carboxyl side of argenine

121
Q

carboxypeptidases

A

enzyme that cleaves on amino side of carboxy-terminal amino acid.

122
Q

Isoelectric focusing

A

separates molecules on the bases of their pI. Tubes with polyelectrodes that migrate to specific points in the tube when in an electric field. Creates pH gradient through tube. Proteins migrate to point in tube where pH corresponds to pI.

123
Q

2D gel electrophoresis

A

Combines isoelectric focusing and SDS-PAGE. Proteins are first separated according to the pI (isoelectric focusing) and then by size (SDS-PAGE). Gives 2D separation of every protein.

124
Q

Considerations in monitoring activity in protein during purification:

A

total protein, total activity, specific activity, yield, purification level

125
Q

(protein purification) Specific activity=

A

total activity/total protein for a given method

126
Q

(protein purification) Yield =

A

total amount of activity at given step/total activity of the first step

127
Q

(protein purification) Purification level =

A

specific activity of a given step/specific activity of the first step.

128
Q

MALDI-TOF

A

determining the molecular weight of relatively large molecules (polypeptides). Sample put in evacuated chamber, laser ionizes creating charged molecule, electric field drives molecules towards detector. Measure time of travel (smaller/lighter = travel faster)

129
Q

The Time of Flight (TOF of MALDI-TOF)

A

allows for determination of mass to within fractions of Daltons. Only specific amino acid combinations can give a specific weight so the sequence combo is found on the computer and can be compared to known sequences of proteins of the organism.

130
Q

Western Blot test

A

Protein separation that involves identification of a specific protein in a mix by SDS-PAGE, transferring it to a membrane, adding an antibody labeled with a color to bind to that protein.

131
Q

HPLC

Ex: Reverse Phase Chromatography

A

chromatography method- separates on basis of polarity.
Reverse phase chromatography: microscopic beads bound to non-polar side chains are in column. Non-polar compounds interact with beads and come down last.

132
Q

X-ray chrystallography

A

Crystal of pure protein (DNA/RNA) subjected to beams of X-rays from all angles. Rays affected by interaction with electron clouds (bent/deflected). Electron density map can come from this to give 3-D coordinates of every atom to within a few Angstroms.

133
Q

NMR

A

Uses magnetic fields. Comes up with structure based on spin of nuclei. Advantage: can give structural information of molecules when they are in aqueous solution.

134
Q

Myoglobin

A

protein responsible for storing oxygen in body. Battery-like capacity in tissues to release oxygen. Can take oxygen from hemoglobin.

135
Q

Structure of myoglobin

A

Single subunit protein that can have porphyrin ring to hold iron and histadine.

136
Q

Hemoglobin

A

protein responsible for carrying oxygen in the body. Carries oxygen from lungs to tissues. Genetically related to myoglobin and evolutionarily derived from it.

137
Q

Structure of hemoglobin

A

four subunit complex (two alpha subunit and two beta subunits). Contains histadine and porphyrin rings to hold iron.

138
Q

Porphyrin rings in myoglobin and hemoglobin

A

Specifically: Protoporphyrin IX. Hold ferrous (Fe2+) iron involved in carrying oxygen. Ferric iron (Fe3+) is oxidized form of iron and will not carry oxygen.

139
Q

Heme

A

term used to describe protoporphryin IX complexed with iron

140
Q

What holds iron in hemoglobin and myoglobin in place?

A

four nitrogens of the protoporphyrin IX ring and a histadine (proximal).

141
Q

What carries oxygen in hemoglobin/myoglobin?

A

carried between iron and an additional histadine (distal) not involved in holding iron.

142
Q

Plot of myoglobin related to affinity for oxygen

A

Plot of percentage of oxygen bound sites vs. partial pressure of myoglobin yields a hyperbolic curve (consistent with high affinity but does not release oxygen easily). P50 (partial pressure of oxygen necessary to fill 50% of myoglobins) is very low.

143
Q

Plot of hemoglobin related to affinity for oxygen

A

Sigmoidal curve because of cooperative fashion of binding.

144
Q

Cooperativity

A

Binding of oxygen by iron atom causes it and attached histadine + amino acids to pull up and change shape. Change in shape results in protein gaining affinity for oxygen as more oxygen is bound.

145
Q

Hemoglobin’s two states

A

Tight state, called T state which exhibits low oxygen binding affinity. Releases oxygen.
Relaxed state, called the R state, which exhibits increased oxygen binding affinity.

146
Q

Binding and release of oxygen flip hemoglobin to what states?

A

Binding flips it from T to R and release of oxygen flips it from R to T

147
Q

2,3-bisphosphoglycerate (2,3-BPG)

A

produced by actively respiring tissues. Bind in the gap in center of hemoglobin, which stabilizes the T state and release of oxygen. Tissues with more 2,3-BPG get more oxygen.

148
Q

2,3 BPG in smokers

A

Smokers have higher concentration of 2,3-BPG in their blood, so have a harder time going to the R-state where they can bind to oxygen.

149
Q

The Bohr effect

A

describes responses to changes in pH with respect to oxygen and CO2. Binding of protons to histidines in the molecule when under low pH causes oxygen effects to arise from changes in tertiary structure of hemoglobin. Greater release of oxygen by hemoglobin.

150
Q

What occurs in rapidly metabolizing tissue?

A

generate low pHs due to release of carbon dioxide and conversion of this to carbonic acid by carbonic anhydrase. Carbonic acid readily loses a proton becoming bicarbonate.

151
Q

What absorbs protons generated by rapidly metabolizing tissues.

A

Hemoglobin

152
Q

CO2 binding to hemoglobin

A

Can be taken up by hemoglobin at amine residues, causing protons to be released. Binds to a site other than where oxygen binds.

153
Q

What does carbon monoxide do?

A

Binds to same site as oxygen in heme group, so it competes with oxygen.

154
Q

How is CO2 gas released in lungs?

A

High oxygen concentration causes oxygen to force off the carbon dioxide and carried protons from hemoglobin. Addition of proton to bicarbonate creates carbonic acid, reversal of carbonic anhydrase reaction causes CO2 gas to be released.

155
Q

How is CO2 gas released in lungs?

A

High oxygen concentration causes oxygen to force off the carbon dioxide and the carried protons from hemoglobin. Addition of proton to bicarbonate creates carbonic acid, reversal of carbonic anhydrase reaction causes CO2 gas to be released.

156
Q

Why does the Bohr effect occur?

A

protons binding to hemoglobin on histidines change charge and favor release of oxygen. Bonding of CO2 (as a carboxyl) to amines also creates same structure that favors release of oxygen.

157
Q

How is fetal hemoglobin different from normal hemoglobin? why?

A

It has two gamma subunits in place of two beta subunits which does not allow it to bind to 2,3 BPG. It remains more in the R-state and has higher affinity for oxygen. This is because it doesn’t have a high oxygen need, doesn’t exercise.

158
Q

Sickle Cell anemia

A

genetic disease when hemoglobin polymerizes under low oxygen conditions causing blood cells to form sickle shapes. Get stuck in capillaries and removed by body causes anemia.

159
Q

Sickle cell anemia effect on malaria

A

Those heterozygous of sickle cell anemia are resistant to malaria.

160
Q

Enzymes

A

proteins that catalyze reactions. Capable of speeding reactions quadrillions of times faster than the same reactions would occur in the absence of enzymes.

161
Q

Non-proteinaceous molecules that bind to enzymes…

A

help enzymes to catalyze reactions and are called coenzymes/cofactors.

162
Q

Gibbs free energy/ change in gibbs free energy

A

the energy available to do useful work in reactions. Change in gibbs free energy determines where reaction in favored/forward (▵G 0), or in equilibrium (▵G = 0).

163
Q

▵Gº’ (standard Gibbs free energy change)

A

gibbs free energy change for reaction under standard conditions. Sign of this DOES NOT tell direction of reaction unless in standard conditions.

164
Q

Activation energy (▵G+)

A

Catalysts act by lower ▵G+ but do not change the overal ▵G of the reaction. They lower the energy required to activate the reaction.

165
Q

Do enzymes change overall reaction concentration at equilibrium?

A

NO. They simply allow the reaction to get to equilibrium faster.

166
Q

Equation to calculate ▵G

A

▵G = ▵Gº’ + RTln[Products/Reactants]

As product concentration increases, ▵G becomes more positive (unfavorable).

167
Q

Velocity of a reaction =

What does the plot look like (velocity vs. substrate concentration)

A

Concentration of product / time
Looks hyperbolic like myoglobin because as substrate increases, so does velocity until it reaches maximum and stays constant.

168
Q

Activation energy (▵G+)

A

Catalysts act by lower ▵G+ but do not change the overall ▵G of the reaction. They lower the energy required to activate the reaction.

169
Q

Part of Michaelis-Menton Model:
Velocity of a reaction =
-What does the plot look like (velocity vs. substrate concentration)

A

Concentration of product / time
-Looks hyperbolic like myoglobin because as substrate increases, so does velocity until it reaches maximum (Vmax) and stays there.

170
Q

Maximum velocity (Vmax)

A

occurs when enzyme is saturated with substrate. Depends on the amount of enzyme used to measure it. NOT a constant for an enzyme.

171
Q

Km

A

The substrate concentration that gives Vmax/2. Vmax varies on amount of enzyme, but Km is a constant for a given enzyme and its given substrate.

172
Q

Does Km = Vmax?

A

No! Km is equal to the substrate concentration where velocity equals Vmax/2.

173
Q

How does Km relate to enzyme affinity for its substrate?

A

Higher Km means lower affinity (it took more substrate to reach Vmax/2 velocity), and lower Km means higher affinity (it took less substrate to reach Vmax/2 velocity).

174
Q

Equilibrium in enzyme reactions:

A

Where relative concentration of products and reactant do not change. Initial velocities of reaction are measured to avoid product to accumulate and favor a reverse reaction.

175
Q

Lineweaver-Burk plot

A

alternative V vs. S plot where inverse is taken. 1/V vs. 1/S plot, making it a straight line.

176
Q

X and Y intercepts of Lineweaver-Burk plot

A

Y intercept is the 1/Vmax, X intercept is -1/Km

177
Q

Are enzymes flexible?

A

Yes.

178
Q

Fischer Lock and Key model

A

Enzymes are inflexible and the substrate is like a key fitting into a lock.

179
Q

Koshland’s model of enzyme action (more accurate)

A

Induced fit model. Enzyme changes substrate but substrate binding to enzyme also changes enzyme which allows it to bring together molecular groups or bind to other molecules. Enzymes orient substrates together for catalysis.

180
Q

Chemical changes in enzymes…

A

are brought about by catalysis and facilitate last change in enzyme shape before releasing product. Enzyme returns to original shape.

181
Q

Kcat

A

= Vmax/[enzyme]
Turnover number, corresponds to the number of molecules of product make per molecule of enzyme per second. Constant for an enzyme.

182
Q

Perfect enzyme

A

Enzymes evolved to the point where any additional mutation will reduce their ability to catalyze reactions. Very high Kcat/Km ratio.

183
Q

Only thing that inhibits ability of perfect enzyme more efficiently is:

A

diffusion of substrate in water.

184
Q

Sequential Displacement subsets:

A

Random Binding- order of binding multiple substrates not rigidly set.
Ordered Binding- Simple ordered binding. One substrate binds then another, then product is released.

185
Q

Substrate binds to enzyme in what type of bond?

A

non-covalent.

186
Q

Double-Displacement (or Ping-Pong kinetics)

A

Enzyme only binds to one substrate at a time, but switches back and forth between different states.

187
Q

Example of double-displacement

A

transaminase flips back and forth between carrying oxygen or carrying an amine group. This affects what substrate it binds to.

Biochemistry 450 (3 decks)

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