Chem 3511 Test 2

Front 1

What is the central dogma?

Back 1

Front 2

What 3 residues make up the catalytic triad?

Back 2

Serine, Histidine, Aspartic Acid

Front 3

What are heat shock proteins made of?

Back 3

Beta sheets or Beta strands

Front 4

NAD(P)H

Back 4

Reduced Form

Front 5

NAD(P)+

Back 5

Oxidized Form

Front 6

What is the Bohr effect?

Back 6

The reduction of hemoglobin's affinity for O2 at low pH.

Blood in tissues is more acidic than blood in the lungs to to higher CO2 conc., so the acidic environment favors dissociation of O2 where it is needed.

Front 7

What is the best measure of an enzyme's efficiency?

Back 7

kcat/Km

Front 8

What is the Michaelis-Menton Equation and what is it used for?

Back 8

Used to characterize enzymes. Vo is measued at various [S], vo is plotted vs [S] to obtain vmax from asymptote. Km is obtained rom the plot when vo = vmax/2.

Front 9

What is competitive inhibition?

Back 9

When the inhibitor binds to the same site as a substrate. Effectively lowers the concentration of the substrate.

Front 10

what is uncompetitive inhibition?

Back 10

When the inhibitor binds to the enzyme substrate complex, effectively lowering the number of enzymes available.

Front 11

What are the 3 stages of a polymerase chain reaction cycle?

Back 11

denaturation, annealing, extension

Front 12

How do enzymes work?

Back 12

Bind the transition state for the reaction, which decreases the activation energy barrier, therby increasing the reaction rate.

Front 13

What is 2-mercaptoethanol used for?

Back 13

Reducing disulfide bonds in proteins.

Front 14

Why does DNA have a major and minor groove?

Back 14

?

Front 15

True or False: Double stranded DNA is antiparallel

Back 15

True

Front 16

T or F: Beta strands in beta sheets can be parallel or andiparallel

Back 16

True

Front 17

T or F: Tertiary amins can both donate and accept hydrogen bonds?

Back 17

F

Front 18

T or F: Dideoxy NTPs are used in Sanger sequencing of DNA

Back 18

T

Front 19

T or F: Myoglobin subunits bind oxygen in a cooperative manner.

Back 19

F

Front 20

T or F: For PCR amplifcation the target sequence to be amplified must be very pure.

Back 20

F

Front 21

T or F: Hydrogen bonding is the major stabilizing force for double stranded DNA.

Back 21

F

Front 22

T or F: Sucrose is a large polymer of glucose resides used for energy storage.

Back 22

F

Front 23

How is an enzymes affinity for a substrate related to Km?

Back 23

Km is used to determine how quickly an enzyme substrate complex dissociates to form a product, so lower Km implies greater affinity and higher implies a lesser affinity.

Front 24

What is the turnover number?

Back 24

The turnover number is kcat or the number of reaction processes that each active site catalyzes per unit time.

Front 25

What is the best measure of enzyme efficiency and why?

Back 25

kcat/Km.

Front 26

How can you tell whether inhibition affects substrate binding or catalytic activity from Lineweaver-Burk plot?

Back 26

Comptetitive: Changes Slope.

Uncompetitive: Changes intercept:

Mixed: Changes both.

Front 27

What are the inactive precursors of protease called?

Back 27

zymogens?

Front 28

Why do mutations such as Arg -> Lys or Leu -> Ile often have little effect on protein function?

Back 28

Since the mutations are conservative(same charge, similiar hydrophobicity, and side chain volume), they do not disrupt the function at most positions in the protein.

Front 29

Oxygen forms a hydrogen bond with _______ when it binds to heme.

Back 29

His E7

Front 30

In the ______ state of hemeglobin, the iron ion is out of the plane of the poryphyrin ring.

Back 30

T or deoxy?

Front 31

The conversion of hemoglobin from the T ro the R state requires breaking of ______ involving C-terminal residues.

Back 31

ion pairs

Front 32

Hemoglobin's subunits bind oxygen in a _______ manner.

Back 32

positively cooperative

Front 33

An increase in pCO2 causes hemoglobin's affinity for oxygen to _________.

Back 33

decrease

Front 34

The absence of 2,3-BPG causes hemoglobin's affinity for oxygen to _________.

Back 34

increase

Front 35

Sickle cell hemoglobin does not form fibers in the ____________ form.

Back 35

R

Front 36

When unstable hemoglbin is degraded; degradation products often cause cell lysis, leading to a condition called _________.

Back 36

hemolytic anemia

Front 37

Mutations that favor the oxidation of the heme iron(II) to iron (III) can cause ______.

Back 37

cyanosis

Front 38

What is cyanosis?

Back 38

a bluish skin color

Front 39

What is the Hill constant?

Back 39

yo2 = (po2)^n/((p50)^n+(pO2)^n) where n is the hill constant.

The hill constant increases with the degree of cooperativity of a reaction.

n>1 -> positively cooperative because O2 binding increases the affinity of hemoglobin for further O2 binding.

Front 40

What happens when the T state of hemoglobin rearranges to the R state?

Back 40

Fe(II) moves into the heme plane

Front 41

T

Back 41

deoxyhemoglobin

Front 42

R

Back 42

oxyhemoglobin

Front 43

How many different classes of antibodies are produced by the human immune system?

Back 43

5

Front 44

What is the approximate weight of an IgG molecule?

Back 44

150 kDa

Front 45

Given that single nucleotide mutations in DNA occur at a constant rate, how does the rate of evolution of different proteins vary?

Back 45

The rate at which proteins accept changes depends upon the function of both (1) the protein and (2) the residue within the protein. Proteins (and amino acids) whose function is highly dependent upon interactions with other proteins (or amino acids) are slow to accept substitutions. Conversely, those with fewer interactions accept more substitutions and evolve more rapidly.

Front 46

Why are protein sequences customarily reconstructed from sequenced fragments?

Back 46

Large polypeptides cannot be directly sequenced.

Front 47

Lysine can form a salt bridge by associating with which nearby residue?

Back 47

Glu

Front 48

alpha helix

Back 48

Right handed

Hydrogen bond fomrs between the carbonyl oxygen of the nth amino acid reside and the -NH gourp of the (n+4)th amino acid reside.

Proline is typlically not found in the helix

there are 3.6 amino acids per turn.

Front 49

Hemoglobin's subunits bind oxygen in a ______ manner.

Back 49

Positively coopertive

Front 50

myglobin and a single chain of hemoglobin have most similiar _____ structures.

Back 50

Tertiary

Front 51

Collagen

Back 51

Contains hydroxylated amino acids

Polypetide forms a left-handed helix

Requires Gly at every 3rd position

Triply helical structure twists in the righ handed direction.

Front 52

Why does globin or heme alone not efficient as an oxygen carrier??

Back 52

O2 binds as an axial ligand to the iron in the heme. O2 will bind heme alone very tightly and will not release O2 in a low pO2 environment. Globin alone will not bind O2 (or very low, not useful affinity)

Front 53

The molecule 2,3-biphosphoglycerate binds to the _____ state of the protein _____.

Back 53

T or deoxy; hemoglobin

Front 54

porphyrin + iron

Back 54

heme

Front 55

What molecules is a cofactor used in oxidation-reduction reactions?

Back 55

NAD+

Front 56

Serine

Back 56

Ser, S

Front 57

Histidine

Back 57

His, H

Front 58

Aspartic Acid

Back 58

Asp, D

Front 59

What is myoglobin's primary physiological role?

Back 59

To facilitate oxygen diffusion

Front 60

The binding of O2 to myoglobin as a function of pO2 is described by what curve?

Back 60

Hyperbolic

Front 61

The binding of O2 to hemoglobin as a function of pO2 is described by what curve?

Back 61

Sigmoidal

Front 62

Label the structure of IgG

Back 62

Front 63

What is the main conclusion from Christian Anfinsen's experiment?

Back 63

A protein's tertiary structure is determined by its primary structure.

Front 64

Types of Enzyme Classifications

Back 64

Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases

Front 65

Oxidoreductates

Back 65

Oxidation-reduction reactions

Front 66

Transferases

Back 66

Transfer of functional groups

Front 67

Hydrolases

Back 67

Hydrolysis reactions

Front 68

Lyases

Back 68

Group elimination to form double bonds

Front 69

Isomerases

Back 69

Isomerization

Front 70

Ligases

Back 70

Bond formation coupled with ATP hydrolysis

Front 71

Types of Catalysis

Back 71

Acid-base, Covalent, Metal ion, Proximity and orientation, preferential binding of the transition state complex

Front 72

Amide bond has _ double bond character.

Back 72

40%

Front 73

3 facts about collagen

Back 73

Fibrous protein

Connective tissues as bone, skin, teeth

gelatin

requires ascorbic acid

Front 74

3 facts about alpha-keratin

Back 74

A coiled-coil

rich in cysteines/disulfide bonds

7-residue pseudorepeat structure

Front 75

What is the function of the oxyanion hole?

Back 75

Stabilizes the anionic tetrahedral intermediate in chymotrypsin/serine proteases

Front 76

Myoglobins secondary structure is primarily composed of _.

Back 76

alpha-helices

Front 77

Max perutz's investigation of the structure of hemoglobin primarily utilized ___.

Back 77

x-ray crystallography

Front 78

IgG is one of five classes of antibodies that can be produced by our immune system. IgGs have a molecular mass of approximately 150 kDa, what is there subunit composition?

Back 78

2 light chains, 2 heavy chains.

Front 79

Describe GroEL/ES general function

Back 79

To bind and refold misfolded proteins (utilizing ATP)

Front 80

Name 2 prion diseases

Back 80

Alzheimer's disease

Mad Cow disease

Front 81

Main conclusion from Christian Anfinsen's experiments on ribonucleae A (RNase)?

Back 81

A protein's tertiary structure is determined by its primary structure.

Front 82

Why do deoxyhemoglobin crystals shatter when exposed to oxygen?

Back 82

Oxygen causes a conformational change that shatters the crystal.

Front 83

What is the Bohr effect in hemoglobin?

Back 83

Oxygen affinity increases with increasing pH.

Front 84

Researchers introduced prions into normal mice and mice that were genetically predisposed todevelop a disease resembling Alzheimer's by expressing the protein Aβ. Speculate on the nature of theprotein Aβ and explain why the Alzheimer's prone mice displayed symptoms of the prion diseasemuch sooner than did the normal mice. (5 pts)

Back 84

Aβ must be a prion protein in the PrPSc form, which is autocatalytic- it induces PrPC to become PrPSc.The brains of the Alzheimer's-prone mice were already burdened with accumulated Aβ , so the PrPScaggregation augmented the brain damage, leading to earlier onset of symptoms than in mice whosebrains were not already damaged by accumulation.

Front 85

[T/F] X-ray diffraction provides data directly on the positions of atomic nucleii.

Back 85

F

Front 86

[T/F] NMR provides a single protein structure.

Back 86

F

Front 87

[T/F] Protein 3° structures can be reliably predicted from their 1° structure.

Back 87

F

Front 88

[T/F] Sickle cell anemia results from a single amino acid substitution in hemoglobin.

Back 88

T

Front 89

[T/F] Transferases cleave C-C, C-O, C-N and other bonds by elimination, leaving double bonds orrings.

Back 89

F

Front 90

[T/F] Antibodies are immunoglobulins.

Back 90

T

Front 91

[T/F] IgGs bind antigens through six hypervariable loops.

Back 91

T

Front 92

[T/F] Immunoglobulins are proteins

Back 92

T

Front 93

In a mutant form of hemoglobin, a Phe residue is present at a position in the sequence where normalhemoglobin has a Glu residue. This mutation causes aggregation of the protein. The aggregation ismost likely due to interactions between molecules.

Back 93

None of the above

Front 94

Which of the following statements is not true of enzyme catalysts?

Back 94

They are generally equally active on both the D and L isomers of a given substrate.

Front 95

Conformation(s) that has (have) both a favorable hydrogen bonding pattern and Φ and Ψ values thatfall within the allowed Ramachandran conformational regions is (are):

Back 95

A. alpha-helix

B. collagen helix

C. beta-sheet

D. None of the above

E. All of the above

Answer: E