Protein Structure and Function

Question 1

The standard amino acids have the same general structure (primary amino group) with the exception of?

Answer 1

Proline (secondary amino group)

Question 2

In proteins, almost all the carbonyl and amino groups are combined through

Answer 2

Peptide linkages/amide bond

Question 3

Amino acids can behave as an acid or base

Answer 3

Amphoteric property

Question 4

When PH > PkA this is ? D

1. Acidic
2. Protonated
3. Amphoteric
4. Deprotonated

Answer 4

Deprotonated (hydrogen has been removed)

Question 5

PkA>PH

Answer 5

Protonated (hydrogen)

Question 6

What are the four classes of amino acids

Answer 6

1. Non polar
2. Uncharged polar
3. Acidic
4. Basic

Question 7

Non polar amino acid with two Hydrogen groups

Answer 7

Glycine (Gly)

Question 8

Non polar amino acid with sulfur

Answer 8

Methionine (Met)

Question 9

Non polar amino acid where the R group interacts with the amino acid

Answer 9

Proline (Pro)

Question 10

1. Non polar amino acid
2. Forms a rigid ring structure because the R group interacts with the amino group, this geometry contributes to the formation of the extended fibroid structure of collagen
3. Interrupts the alpha helices in more compact proteins

Answer 10

Proline

Question 11

* This is caused by the substitution of the polar glutamate by non polar valine at the 6th position of the beta subunit of hemoglobin A
* replaces acidic amino acid with a non polar amino acid

Answer 11

Sickle cell anemia

Question 12

Uncharged Amino Acids will have hydroxyl (OH), Amide ( C=O NH2), or sulfhydryl groups (SH)

Answer 12

STT

Serine (Ser)
Threorine (Thr)
Tyrosine (Tyr)

Question 13

Uncharged polar amino acids that serve as attachment site for structures like phosphate groups

Answer 13

Hydroxyl

Question 14

Uncharged polar amino acids that serve as attachment sites for oligosaccharide chains in glycoproteins

Answer 14

Amide and hydroxyl groups

Question 15

Uncharged polar amino acids that serve as important components of the active site of enzymes

Answer 15

Sulfhydryl groups

AA - Methionine & Cysteine

Question 16

What are the two acidic amino acids, contain a negatively charged (COO-) group. Proton donors

Answer 16

GA

Aspartate (Asp)
Glutamate (Glu)

Question 17

What are the basic amino acids?

Side chains are fully ionized and positively charged

Proton acceptors

Answer 17

LAH

Lysine (Lys)
Arginine (Arg)
Histidine (His)

Question 18

Amino Acid abbreviations

Question 19

Amino acids not produced by the body

Answer 19

Essential - ACGPST

Question 20

Amino acids produced by the body

Answer 20

Nonessential

Question 21

Pair of compounds with exactly the same connectivity but opposite three-dimensional shapes

Answer 21

Enantiomers

Question 22

• Rotate a plane of polarized light in the opposite direction
• Mirror images (cannot be superimposed on each other)

Answer 22

Optical isomers

Question 23

Brønsted-Lowry acid

Answer 23

Proton donor

Question 24

Brønsted-Lowry base

Answer 24

Proton acceptor

Question 25

The larger the Ka, smaller the pKa

Answer 25

Strong acid

Question 26

The smaller the Ka and larger the pKa

Answer 26

The weaker the acid

Question 27

Formulas

Answer 27

``` Ka= [H+] [A-]/[HA] PkA = -log Ka Ph = -log [H+] ```

Question 28

Henderson-Hasselbalch equation

Answer 28

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

Question 29

PH\>pKa Log of \>1 is positive

Answer 29

Deprotonated species (A-) dominates

Question 30

PH less than pKa

Answer 30

Protonated (HA) dominates

Question 31

What is the charge on the AA arginine at physiologic pH? D 1. -2 2. -1 3. 0 4. +1 5. +2

Answer 31

+1

Question 32

At physiologic pH, the amino group and carboxyl group of the AA form what charges? A 1. +1, -1 respectively 2. -1, +1 respectively 3. 0, 0 4. 0, -1 respectively 5. -1, 0 respectively

Answer 32

+1, -1 respectively

Question 33

T or F: The general structure of an AA contains a chiral carbon with a carboxyl group, secondary amine, hydrogen, and R group attached. F because it’s a primary amine

Answer 33

False, because it is a primary amine

Question 34

Which of the following AA will you NOT likely find in an alpha-helix?B 1. Cysteine 2. Proline 3. Methionine 4. Valine 5. Glutamine

Answer 34

Proline

Question 35

The pH at which a molecule possesses no net charge is called: A 1. Isoelectric Point 2. Optimal pH 3. Maximum Buffering Capacity 4. Physiologic pH 5. Extreme pH

Answer 35

Isoelectric Point

Question 36

T or F Ka is defined as the dissociation constant of an acid. Therefore, the higher the Ka, the stronger the acid; the higher the pKa, the weaker the acid. T

Answer 36

True

Question 37

When does maximum buffering capacity occur? B 1. When the molecule has no net charge? 2. When pH=pKa 3. When the molecule has a positive charge 4. When pH\>pKa 5. None of the above

Answer 37

When pH=pKa

Question 38

Which of the following is the most abundant protein in the body? A 1. Collagen 2. Elastin 3. a-Ketain 4. Hemoglobin 5. Myoglobin

Answer 38

Collagen

Question 39

Which of the following is the correct order of collagen synthesis? A 1. Procollagen, Tropocollagen, Collagen 2. Tropocollagen, Procollagen, Collagen 3. Collagen, Tropocollagen, Procollagen 4. Procollagen, Collagen, Tropocollagen 5. None of the above

Answer 39

Procollagen, Tropocollagen, Collagen

Question 40

Where would you find Tropocollagen? D 1. Golgi 2. Rough Endoplasmic Reticulum 3. Nucleus 4. Extracellular Matrix 5. Lysosomes

Answer 40

Extracellular Matrix

Question 41

Which of the following ligands increases the affinity of hemoglobin for oxygen? D 1. H+ 2. 2,3-BPG 3. CO2 4. CO 5. All of the above

Answer 41

CO - carbon monoxide

Question 42

Which bonds are found in the primary structure of proteins? D 1. Amide 2. Peptide 3. Hydrogen bonds 4. A, B 5. A, B, C

Answer 42

Amide & Peptide

Question 43

Which bonds are found in the secondary structure of proteins? C 1. Amide 2. Peptide 3. Hydrogen bonds 4. A, B 5. A, B, C

Answer 43

Hydrogen Bonds

Question 44

Which bonds/interactions are are found between the side chains (R groups) in the tertiary structure of proteins? E 1. Hydrogen bonds 2. Disulfide bonds 3. Ionic Interactions 4. Hydrophobic Interactions 5. All of the above

Answer 44

All of the above

Question 45

Which of the following diseases are caused by the prion protein (PrP)? C 1. Alzheimer disease 2. Parkinson disease 3. Creutzfeldt-Jakob disease 4. A, B 5. Proteins don’t cause diseases

Answer 45

Creutzfeldt-Jakob disease

Question 46

Amyloids (tau protein affected in the beta-pleated sheets) have been implicated in neurodegenerative disorders such as: D 1. Alzheimer disease 2. Parkinson disease 3. Creutzfeldt-Jakob disease 4. A, B 5. Proteins don’t cause diseases

Answer 46

A & B

Question 47

How many molecules of O2 can be transported by hemoglobin? D D 1. 1 2. 2 3. 3 4. 4 5. 5

Answer 47

4

Question 48

How many molecules of O2 can be transported by myoglobin? D D 1. 1 2. 2 3. 3 4. 4 5. 5

Answer 48

1

Question 49

Decreased production of normal hemoglobin is characterized by: D 1. sickle-cell anemia (Hb S) 2. Hemoglobin C disease 3. Hemoglobin SC disease 4. Thallassemia syndromes 5. None of the above

Answer 49

Thallassemia syndrome

Question 50

When a substrate itself serves as an effector, it is referred to as a: C 1. Negative effector 2. Positive effector 3. Homotropic effector 4. Heterotropic effector 5. All of the above

Answer 50

Homotropic effector

Question 51

Which of the following AA would likely serve as an attachment site for a phosphate group? D 1. Serine 2. Threonine 3. Tyrosine 4. All of the above 5. None of the above

Answer 51

All of the above

Question 52

what enzyme adds a phosphate group?

Answer 52

Kinase

Question 53

What enzyme hydrolyzes peptide bonds?

Answer 53

Peptidases (Proteases)

Question 54

proteins that perform the same function but have different primary structures

Answer 54

Isoforms

Question 55

protein isoforms that function as enzymes

Answer 55

Isozymes

Question 56

* Reservoir for oxygen * oxygen carrier that increases the rate of transport of oxygen within the muscle cell

Answer 56

Myoglobin

Question 57

* Transports oxygen from the lungs to the capillaries of tissues * It can also transport hydrogen and carbon dioxide from the tissues to the lungs

Answer 57

Hemoglobin

Question 58

These ligands stabilize the taut state (deoxygenated form) of hemoglobin and this leads to a decreased affinity for oxygen (right shift) 1. increased H+ (low pH) 2. Increased 2,3-bisphosphoglycerate 3. Increased carbon dioxide 4. increased carbon monoxide

Answer 58

1. increased H+ (pH) 2. Increased 2,3-bisphosphoglycerate 3. Increased carbon dioxide

Question 59

Most abundant protein in the body, composed of 3 polypeptide helices

Answer 59

Collagen

Question 60

What are the markers of collagen that are not present in other proteins 1. Glycine 2. Hydroxyproline 3. Hydroxylysine 4. two of the options

Answer 60

1. Hydroxyproline 2. Hydroxylysine

Question 61

Where would you find Procollagen? D 1. Golgi 2. Rough Endoplasmic Reticulum 3. Nucleus 4. Extracellular Matrix 5. Lysosomes

Answer 61

Rough Endoplasmic Reticulum

Question 62

This collagen genetic mutation results in fragile stretchy skin and loose joints 1. Osteogenesis imperfects 2. Ehlers-Danlos syndeom (EDS) 3. Sickle Cell disease 4. Alzheimer's disease

Answer 62

Ehlers-Danlos syndeom (EDS)

Question 63

Protein catalysts that increase the rate of reactions without being changed in the overall process

Answer 63

Enzymes

Question 64

RNAs with catalytic activity , much less encountered than protein catalysts

Answer 64

Ribozymes

Question 65

enzyme that requires ATP

Answer 65

Synthetase

Question 66

Enzyme that does not require ATP

Answer 66

Synthase

Question 67

Enzyme that removes a phosphate group

Answer 67

Phopshatase

Question 68

Enzyme that breaks bonds by using inorganic phosphate

Answer 68

Phyosphorlyase

Question 69

Adds a phosphate group form a high energy molecules such as ATP

Answer 69

Kinase

Question 70

Enzyme that catalyzes oxidation - reduction reactions using oxygen as the electron acceptor but oxygen atoms are not incorporated into substrate

Answer 70

Oxidase

Question 71

Enzyme that oxidizes a sub substrate by transferring oxygens to it

Answer 71

Oxygenase

Question 72

This contains the AA side chains that participate in substrate binding and catalysis

Answer 72

Active site

Question 73

Enzyme that interacts with one or a few substrates and catalyzing only one type of reaction

Answer 73

specific

Question 74

Enzyme with its nonprotein component (active)

Answer 74

Holoenzyme

Question 75

Enzyme without its nonprotein component (active) - magensium/zinc

Answer 75

Apoenzyme

Question 76

Nonprotein moeity (inorganic or organic) of the enzyme

Answer 76

cofactor

Question 77

nonprotein moeity (small inorganic molecule). Frequently derived from vitamins (i.e. NAD+ from niacin and FAD from riboflavin)

Answer 77

Coenzyme

Question 78

Coenzymes that are permanently associated with the enzyme

Answer 78

Prosthetic group

Question 79

Coenzymes that are only transiently associated with the enzyme

Answer 79

Cosubstrate

Question 80

Enzymes that change their conformation when bound by an effector at a site other than actives site 1. Cosubstrate enzymes 2. Prosthetic enzymes 3. Allosteric Enzymes 4. Apoenzyme

Answer 80

Allosteric Enzymes

Question 81

Which factors affect reaction velocity (speed of a reaction) 1. Substrate concentration 2. Temperatirs 3. pH 4. Acid/base 5. three of the above

Answer 81

Increasing 1. Substrate concentration 2. Temperatirs 3. pH

Question 82

What will reflect a low affinity of enzyme for the substrate 1. Large Km 2. Small Km

Answer 82

Large Km

Question 83

What is related order of reaction with respect to the substrate when: * When [S] is much less than Km * V is proportional to [S]

Answer 83

First Order

Question 84

What is related order of reaction with respect to the substrate when: * When [S] is greater Km * V is constant and independent of [S]

Answer 84

Zero Order

Question 85

Any substance that can diminish the velocity of an enzyme-catalyzed reaction is called an 1. Apoenzyme 2. Inhibitor 3. Holoenzyme 4. coenzyme

Answer 85

Inhibitor

Question 86

Reversible inhibitors typically bind to enzymes through 1. covalent bonds 2. hydrogen bonds 3. noncovalent bonds 4. Hydrophobic bonds

Answer 86

noncovalent bonds

Question 87

Irreversible inhibitors typically bind to enzymes through 1. covalent bonds 2. hydrogen bonds 3. noncovalent bonds 4. Hydrophobic bonds

Answer 87

covalent bonds

Question 88

In competitive inhibition, what happens? 1. Km increases, Vmax is unchanged and affinity decreases 2. Km decreases, Vmax increases and affinity decreaes 3. Km is unchanged, Vmax is decreases and affinity increases 4. All the above

Answer 88

Km increases, Vmax is unchanged and affinity decreases

Question 89

In noncompetitive inhibition, what happens? 1. Km increases, Vmax is unchanged and affinity decreases 2. Km decreases, Vmax increases and affinity decrease 3. Km is unchanged, Vmax is decreases and affinity increases 4. All the above

Answer 89

Km is unchanged, Vmax is decreases and affinity increases

Question 90

EffEffCE 1. Negative effector 2. Positive effector 3. Homotropic effector 4. Heterotropic effector 5. All of the above