Test 1 Review

Question 1

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

Answer 1

C. Hydrophobic effect

Question 2

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

Answer 2

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

Question 3

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

Answer 3

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

Question 4

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

Answer 4

7 and 7, and 1x10-7

Question 5

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-]?

Answer 5

Both are 1x10-7

Question 6

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

Answer 6

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

Question 7

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

A. 5

B.10

C.15

D.20

Answer 7

A. 5

Question 8

Which of the following is an essential amino acid?

A. Tyrosine

B. Alanine

C. Threonine

D. Glycine

Answer 8

C. Threonine

Question 9

Which of the following is a BCAA?

A. Valine

B. Histidine

C. Tryptophan

D. Phenylalanine

Answer 9

A. Valine

Question 10

Which amino acids contain sulfur?

Answer 10

Methionine, Cysteine,

Question 11

Which amino acids are aromatic?

Answer 11

Phenylalanine, Tyrosine, Tryptophan

Question 12

Which amino acids are negatively charged?

Answer 12

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

Question 13

Which amino acids are positively charged?

Answer 13

Histidine, Arginine, Lysine (Bases)

Question 14

Which amino acids contain a Hydroxyl group?

Answer 14

Serine, Threonine, Tyrosine

Question 15

What defines homology across species (similar function)?

Answer 15

Orthologs

Question 16

What defines homology within a species but different functions?

Answer 16

Paralogs

Question 17

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?

Answer 17

% identical:40

% similar: 20

% homologous: 60

invarient regions: identical regions (no range)

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

Question 18

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

Answer 18

phi

Question 19

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

Answer 19

psi

Question 20

An alpha helix has how many amino acids per turn?

Answer 20

3.6 (5.4/1.5=3.6)

Question 21

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

Answer 21

Beta Strand

Question 22

What type of protein structure primarily composes hemoglobin?

Answer 22

Alpha helix.

Question 23

What is neccessary for erythrocyte production?

Answer 23

Folic acid, B12, B6

Question 24

Why is free iron in the blood toxic?

Answer 24

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

Question 25

Are alpha helixes typically left or right handed?

Answer 25

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

Question 26

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

Answer 26

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

Question 27

The attached picture represents what type of symmetry?

Answer 27

C3, cyclic symmetry

Question 28

Which of the following is not a condition under which protein denaturation occurs? A. Heat B. substrate binding C. Agitation D. pH extremes

Answer 28

B. substrate binding Heat, pH extremes, Agitation

Question 29

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

Answer 29

reverses misfolds as proteins are transported across membranes.

Question 30

What are the two models of chaperonins?

Answer 30

Active and Passive

Question 31

The passive model of chaperonins process involves:

Answer 31

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

Question 32

Active model of chaperonins involves:

Answer 32

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

Question 33

Hemoglobin is considered a: A. Dimer B. Tetramer C. Epidimer D. Quadtramer

Answer 33

B. Tetramer (four globin chains)

Question 34

A globin chain consists of how many alpha helicies? A. 5 B. 7 C. 8 D. 9

Answer 34

C. 8

Question 35

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

Answer 35

D. F8, histidine

Question 36

Which amino acid in the globin is named the distal histidine? A. F7 B. F8 C. E7 D. E8

Answer 36

C. E7

Question 38

When non-polar molecules come together, this is the effect of: A. Enthalpy B. Entropy C. Spontaneity D. Vander walls forces

Answer 38

B. Entropy

Question 39

Do amino groups have a high or low pKa?

Answer 39

High

Question 40

Do Carbonyl groups have a high or low pKa?

Answer 40

low

Question 41

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

Answer 41

Water

Question 42

What defines the secondary structure elements of a protein?

Answer 42

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

Question 43

Which bond in the peptide sequence has no rotation? A. Alpha carbon bond (N-C) B. Peptide bond (N-C=O)

Answer 43

B. Peptide bond (N-C=O)

Question 44

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

Answer 44

False

Question 45

a kinase will dephosphorlyate or phosphorylate a target?

Answer 45

phosphorylate

Question 46

Peptide bonds are typically in trans or cis conformation?

Answer 46

trans

Question 47

Average number of amino acids in a helix is? A. 10 B. 11 C. 12 D. 13

Answer 47

12

Question 48

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

Answer 48

A. 100 360/3.6 = 100 (helical wheel)

Question 49

Tortional angles in an alpha helix are typically? A. 100 to 100 B. -60 to -60 C. 80 to 80 D. -70 to -70

Answer 49

B. -60 to -60

Question 50

Which of the following destabilize the alpha helix? A. Phenylalanine B. Tryptophan C. Alanine D. Proline

Answer 50

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

Question 51

What is the average length of a beta strand?

Answer 51

4-5

Question 52

How many strands make up a sheet?

Answer 52

2 or more

Question 53

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

Answer 53

A. i1 and i3

Question 54

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

Answer 54

true

Question 55

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

Answer 55

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

Question 56

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

Answer 56

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

Question 57

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

Answer 57

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

Question 58

The tertiary structure is defined by:

Answer 58

the folding of the secondary structures

Question 59

Protein folding is considered highly cooperative because:

Answer 59

it doesnt need chaperones. Happens spontaneously.

Question 60

Hierarchical folding of proteins refers to:

Answer 60

Regions folding independently

Question 61

The molten globule is:

Answer 61

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

Question 62

Relative frequency is:

Answer 62

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

Question 63

Glycine is considered destabilizing because:

Answer 63

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

Question 64

Metamorphic protein refers to:

Answer 64

a protein that exists in multiple states

Question 65

IUPs are:

Answer 65

intrinsically unstructured proteins

Question 66

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

Answer 66

deoxygenated - R state=relaxed or READY to receive

Question 67

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

Answer 67

oxygenated, ready to THROW the oxygen off

Question 68

What is Anemia?

Answer 68

low red blood cell count - cancer patients

Question 69

The episurface in hemoglobin is reffering to?

Answer 69

the elbows, example: FG-C switch interraction

Question 70

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

Answer 70

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

Question 71

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

Answer 71

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

Question 72

How many kelation points does deoxygenated hemoglobin have?

Answer 72

5 kelation points 4 from the heme group, 1 from F8. oxygen is the 6th kelation point. (when attached)

Question 73

What types of hemoglobin does the fetus have?

Answer 73

gamma and alpha

Question 74

What types of hemoglobin does an adult have?

Answer 74

alpha and beta (some delta ~2%)

Question 75

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

Answer 75

typically the beta.

Question 76

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

Answer 76

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

Question 77

Protein turnover refers to:

Answer 77

production and degratation of proteins.

Question 78

Proteins are stabilized by:

Answer 78

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

Question 79

UPR stands for:

Answer 79

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

Question 80

UPR begins where:

Answer 80

the ER

Question 81

What are two chaotropic agents?

Answer 81

UREA and GUANIDINIUM (chemicals that destabilize proteins)

Question 82

What are the types of chemicals that destabilize proteins?

Answer 82

Detergents Chaotropic agents (urea and guanidinium) Organic Solvents (like alcohols)

Question 83

When does PDI apply?

Answer 83

When a protein has wrong disulfide linkages. Stands for Protein Disulfide Isomerases

Question 84

When does PPI apply?

Answer 84

When a protein is in the wrong cis/trans conformation. Stands for: Protein cis-trans proxylisomerases

Question 85

Met hemoglobin refers to:

Answer 85

Iron in the Fe3+ state

Question 86

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

Answer 86

Higher

Question 87

Which of the following have a negative allosteric modification on hemoglobin? A. H+ B. CO2 C. 2,3 BPG

Answer 87

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.

Question 88

Amyloid plaques form through:

Answer 88

nucleation, fibril formation, deposits

Question 89

Lewy bodies are:

Answer 89

larger plaques, encapsulated

Question 90

Do the large or small aggregates cause damage?

Answer 90

small