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Biochem - Heckert > Test 1 Review > Flashcards

Test 1 Review Flashcards

1
Q

What property of water is the fundamental reason for the manifestation of it’s unique properties?

A. Polarity of the molecule

B. Cohesiveness of the molecule

C. Hydrophobic effect of the molecule

D. Free Ions

A

C. Hydrophobic effect

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2
Q

The Free energy of a reaction indicates:

A. The velocity of a reaction

B. Whether a reaction will proceed

C. How easy a reaction occurs

D. How much energy is let loose during a reaction

A

B. Whether a reaction will proceed (negative is spontaneous)

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3
Q

In a Oxidation-Reduction Reaction:

A. A oxidizing agent will reduce the electron acceptor

B. The electron donor will oxidize the electron acceptor

C. The Reducing agent will oxidize the electron acceptor

D. The electron donor will reduce the electron acceptor

A

D. The electron donor (reducing agent) will reduce the electron acceptor (oxidizing agent)

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4
Q

If -log{H+]=7, what is the PH, the POH, and [H+]?

A

7 and 7, and 1x10-7

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5
Q

The equilibrium constant (K) for the dissociation of water is defined as K = [H+][OH−]/[H2O] and has a value of K = 1.8 × 10−16, units of molarity (M) are assumed. The concentration of water in pure water is 55.5 M. What is the [H+], [OH-]?

A

Both are 1x10-7

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6
Q

pKa for phenophthalein is 10 at room temp. Calculate the ratio of its anionic form to acid form at a pH of 8.

A

log(1/100)=-2. therefore the ratio of the base/acid is 1/100.

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7
Q

How many kCal are there for every 100 angstroms of contact area in the hydrophobic effect?

A. 5

B.10

C.15

D.20

A

A. 5

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8
Q

Which of the following is an essential amino acid?

A. Tyrosine

B. Alanine

C. Threonine

D. Glycine

A

C. Threonine

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9
Q

Which of the following is a BCAA?

A. Valine

B. Histidine

C. Tryptophan

D. Phenylalanine

A

A. Valine

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10
Q

Which amino acids contain sulfur?

A

Methionine, Cysteine,

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11
Q

Which amino acids are aromatic?

A

Phenylalanine, Tyrosine, Tryptophan

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12
Q

Which amino acids are negatively charged?

A

Glutamic acid, Aspartic Acid (acids) (Aspartate and Glutamate)

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13
Q

Which amino acids are positively charged?

A

Histidine, Arginine, Lysine (Bases)

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14
Q

Which amino acids contain a Hydroxyl group?

A

Serine, Threonine, Tyrosine

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15
Q

What defines homology across species (similar function)?

A

Orthologs

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16
Q

What defines homology within a species but different functions?

A

Paralogs

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17
Q

V S L I D H P A M T

E R L I E Y Q A M Y

What is the % identical? % similar? % homology? What areas are invarient? What areas are hypervariable? What areas have tolerable mutations?

A

% identical:40

% similar: 20

% homologous: 60

invarient regions: identical regions (no range)

hypervariable: negative ,blosum-62 regions (ex. first two)

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18
Q

The torsion angle around the N-C bond is known as the?

A

phi

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19
Q

The torsion angle around the C-C bond is known as the:

A

psi

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20
Q

An alpha helix has how many amino acids per turn?

A

3.6 (5.4/1.5=3.6)

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21
Q

An antibody would most likely be made primarily of what type of protein structure?

A

Beta Strand

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22
Q

What type of protein structure primarily composes hemoglobin?

A

Alpha helix.

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23
Q

What is neccessary for erythrocyte production?

A

Folic acid, B12, B6

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24
Q

Why is free iron in the blood toxic?

A

catalytically produces free radicals as it shifts from Fe2+ and Fe3+

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25
Q

Are alpha helixes typically left or right handed?

A

Right, left is very rare. Example of left handed helix: Collagen (because of PRO and GLY)

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26
Q

What makes a protein functionally intact in it’s native conformation?

A

Hydrophobic effects, Quaternary structure, Disulfyde bonds (extracellular proteins - two cysteines)

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27
Q

The attached picture represents what type of symmetry?

A

C3, cyclic symmetry

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28
Q

Which of the following is not a condition under which protein denaturation occurs?

A. Heat

B. substrate binding

C. Agitation

D. pH extremes

A

B. substrate binding

Heat, pH extremes, Agitation

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29
Q

What is the function of the molecular chaperone HSP 70?

A. structure of the ribosome

B. Transcription factor

C. Reverses misfolds in proteins

D. membrane denaturation

A

reverses misfolds as proteins are transported across membranes.

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30
Q

What are the two models of chaperonins?

A

Active and Passive

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31
Q

The passive model of chaperonins process involves:

A

exloring until it finds the right point. Example: putting a kid in a time-out.

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32
Q

Active model of chaperonins involves:

A

basket continually interracting with the protein until it gets the proper fold.

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33
Q

Hemoglobin is considered a:

A. Dimer

B. Tetramer

C. Epidimer

D. Quadtramer

A

B. Tetramer (four globin chains)

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34
Q

A globin chain consists of how many alpha helicies?

A. 5

B. 7

C. 8

D. 9

A

C. 8

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35
Q

On the globin chain, which helic point kelates the iron and what amino acid is it?

A. F7, cysteine

B. F7, histidine

C. E8, cysteine

D. F8, histidine

A

D. F8, histidine

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36
Q

Which amino acid in the globin is named the distal histidine?

A. F7

B. F8

C. E7

D. E8

A

C. E7

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37
Q
A
38
Q

When non-polar molecules come together, this is the effect of:

A. Enthalpy

B. Entropy

C. Spontaneity

D. Vander walls forces

A

B. Entropy

39
Q

Do amino groups have a high or low pKa?

A

High

40
Q

Do Carbonyl groups have a high or low pKa?

A

low

41
Q

What is released when a poly-peptide bond is formed?

A

Water

42
Q

What defines the secondary structure elements of a protein?

A

Backbone H-bonding (N-C-C-N…. repeating..)

43
Q

Which bond in the peptide sequence has no rotation?

A. Alpha carbon bond (N-C)

B. Peptide bond (N-C=O)

A

B. Peptide bond (N-C=O)

44
Q

True or False: The R groups in an alpha helix are involved in H-bonding?

A

False

45
Q

a kinase will dephosphorlyate or phosphorylate a target?

A

phosphorylate

46
Q

Peptide bonds are typically in trans or cis conformation?

A

trans

47
Q

Average number of amino acids in a helix is?

A. 10

B. 11

C. 12

D. 13

A

12

48
Q

Every how many degrees in an alpha helix do you have an amino acid with R groups projected OUT?

A. 100

B. 90

C. 80

D. 5.4

A

A. 100

360/3.6 = 100 (helical wheel)

49
Q

Tortional angles in an alpha helix are typically?

A. 100 to 100

B. -60 to -60

C. 80 to 80

D. -70 to -70

A

B. -60 to -60

50
Q

Which of the following destabilize the alpha helix?

A. Phenylalanine

B. Tryptophan

C. Alanine

D. Proline

A

D. Proline (nitrogen unable to participate in H bonding)

51
Q

What is the average length of a beta strand?

A

4-5

52
Q

How many strands make up a sheet?

A

2 or more

53
Q

In the beta turn which of the following bind?

A. i1 and i3

B. i1 and i2

C. i3 and i4

D. i5 and i6

A

A. i1 and i3

54
Q

True or false: proteins typically are either globular or fibrous?

A

true

55
Q

The coiled-coiled stand is typicalled associated with what, which way is it coiled, and how many turns per coil?

A

Alpha-keratin, right haneded, 3.5 residues per turn (repeated heptad sequence)

56
Q

The typically collagen sequence is? Is it an alpha helix?

A

Ex-Pro-Gly, NOT an alpha helix, left handed

57
Q

In the coiled-coiled structure, why is typically found at the A and D sites?

A

Leucine (hydrophobic), G and E sites are typically positively(basic) or negative(acidic) amino acids.

58
Q

The tertiary structure is defined by:

A

the folding of the secondary structures

59
Q

Protein folding is considered highly cooperative because:

A

it doesnt need chaperones. Happens spontaneously.

60
Q

Hierarchical folding of proteins refers to:

A

Regions folding independently

61
Q

The molten globule is:

A

Protein not fully formed yet. Slight adjustments to get to final form.

62
Q

Relative frequency is:

A

The frequency of that form/average freqency of all 20 amino acids.

63
Q

Glycine is considered destabilizing because:

A

It has no R group so psi and phi bonds are able to freely rotate.

64
Q

Metamorphic protein refers to:

A

a protein that exists in multiple states

65
Q

IUPs are:

A

intrinsically unstructured proteins

66
Q

Hemoglobin, when in the R form, is deoxygenated or oxygenated?

A

deoxygenated - R state=relaxed or READY to receive

67
Q

Hemoglobin, when in the T state, is deoxygenated or oxygenated?

A

oxygenated, ready to THROW the oxygen off

68
Q

What is Anemia?

A

low red blood cell count - cancer patients

69
Q

The episurface in hemoglobin is reffering to?

A

the elbows, example: FG-C switch interraction

70
Q

What is the function of the E7 histidine, and what is it called?

A

Protection against carbon monoxide from competition w/ oxygen decreased by 100 fold. The distal histidine.

71
Q

What is the function of the F8 histidine, and what is it called?

A

kelates the IRON. 5th kelation point. Proximal histidine.

72
Q

How many kelation points does deoxygenated hemoglobin have?

A

5 kelation points

4 from the heme group, 1 from F8.

oxygen is the 6th kelation point. (when attached)

73
Q

What types of hemoglobin does the fetus have?

A

gamma and alpha

74
Q

What types of hemoglobin does an adult have?

A

alpha and beta (some delta ~2%)

75
Q

Does oxygen typically bind to the alpha or beta helix first?

A

typically the beta.

76
Q

An increase in H+ concentration would decrease or increase hemoglobin affinity for oxygen.

A

Increased H+, decreases it’s affinity, allowing more oxygen to be unloaded in the cells. The curve shifts to the right.

77
Q

Protein turnover refers to:

A

production and degratation of proteins.

78
Q

Proteins are stabilized by:

A

hydrophobic effects, quaternary structures (oligiomeric structures), and extracellularilly disulfide bonds.

79
Q

UPR stands for:

A

Unfolded Protein Response

also known as UPS - Stress - it occurs when the unfolded protein is unable to go back to its native form.

80
Q

UPR begins where:

A

the ER

81
Q

What are two chaotropic agents?

A

UREA and GUANIDINIUM (chemicals that destabilize proteins)

82
Q

What are the types of chemicals that destabilize proteins?

A

Detergents

Chaotropic agents (urea and guanidinium)

Organic Solvents (like alcohols)

83
Q

When does PDI apply?

A

When a protein has wrong disulfide linkages. Stands for

Protein Disulfide Isomerases

84
Q

When does PPI apply?

A

When a protein is in the wrong cis/trans conformation.

Stands for: Protein cis-trans proxylisomerases

85
Q

Met hemoglobin refers to:

A

Iron in the Fe3+ state

86
Q

Myoglobin has a higher or lower affinity for oxygen than hemoglobin?

A

Higher

87
Q

Which of the following have a negative allosteric modification on hemoglobin?

A. H+

B. CO2

C. 2,3 BPG

A

A, B, C

H+ and CO2 force hemoglobin into the deoxygenated state - BOHR effect

2,3 BPG drives hemoglobin into the T state, ready to throw the oxygen off at the given site. 2,3 BPG is elevated at high altitudes.

88
Q

Amyloid plaques form through:

A

nucleation, fibril formation, deposits

89
Q

Lewy bodies are:

A

larger plaques, encapsulated

90
Q

Do the large or small aggregates cause damage?

A

small

Biochem - Heckert (6 decks)

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