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Biomedical Sciences & Oral Ecosystems I > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

1
Q

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

A

Proline (secondary amino group)

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2
Q

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

A

Peptide linkages/amide bond

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3
Q

Amino acids can behave as an acid or base

A

Amphoteric property

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4
Q

When PH > PkA this is ? D

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

Deprotonated (hydrogen has been removed)

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5
Q

PkA>PH

A

Protonated (hydrogen)

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6
Q

What are the four classes of amino acids

A
  1. Non polar
  2. Uncharged polar
  3. Acidic
  4. Basic
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7
Q

Non polar amino acid with two Hydrogen groups

A

Glycine (Gly)

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8
Q

Non polar amino acid with sulfur

A

Methionine (Met)

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9
Q

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

A

Proline (Pro)

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10
Q
  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
A

Proline

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11
Q

* 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

A

Sickle cell anemia

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12
Q

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

A

STT

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

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13
Q

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

A

Hydroxyl

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14
Q

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

A

Amide and hydroxyl groups

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15
Q

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

A

Sulfhydryl groups

AA - Methionine & Cysteine

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16
Q

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

A

GA

Aspartate (Asp)
Glutamate (Glu)

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17
Q

What are the basic amino acids?

Side chains are fully ionized and positively charged

Proton acceptors

A

LAH

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

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18
Q

Amino Acid abbreviations

A
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19
Q

Amino acids not produced by the body

A

Essential - ACGPST

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20
Q

Amino acids produced by the body

A

Nonessential

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21
Q

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

A

Enantiomers

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22
Q
  • Rotate a plane of polarized light in the opposite direction
  • Mirror images (cannot be superimposed on each other)
A

Optical isomers

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23
Q

Brønsted-Lowry acid

A

Proton donor

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24
Q

Brønsted-Lowry base

A

Proton acceptor

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25
Q

The larger the Ka, smaller the pKa

A

Strong acid

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26
Q

The smaller the Ka and larger the pKa

A

The weaker the acid

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27
Q

Formulas

A 
Ka= [H+] [A-]/[HA]
PkA = -log Ka
Ph = -log [H+]
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28
Q

Henderson-Hasselbalch equation

A

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

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29
Q

PH>pKa
Log of >1 is positive

A

Deprotonated species (A-) dominates

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30
Q

PH less than pKa

A

Protonated (HA) dominates

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31
Q

What is the charge on the AA arginine at physiologic pH? D

  1. -2
  2. -1
  3. 0
  4. +1
  5. +2
A

+1

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32
Q

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
A

+1, -1 respectively

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33
Q

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

A

False, because it is a primary amine

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34
Q

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
A

Proline

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35
Q

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
A

Isoelectric Point

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36
Q

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

A

True

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37
Q

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
A

When pH=pKa

38
Q

Which of the following is the most abundant protein in the body? A

  1. Collagen
  2. Elastin
  3. a-Ketain
  4. Hemoglobin
  5. Myoglobin
39
Q

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
A

Procollagen, Tropocollagen, Collagen

40
Q

Where would you find Tropocollagen? D

  1. Golgi
  2. Rough Endoplasmic Reticulum
  3. Nucleus
  4. Extracellular Matrix
  5. Lysosomes
A

Extracellular Matrix

41
Q

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
A

CO - carbon monoxide

42
Q

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
A

Amide & Peptide

43
Q

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
A

Hydrogen Bonds

44
Q

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
A

All of the above

45
Q

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
A

Creutzfeldt-Jakob disease

46
Q

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
47
Q

How many molecules of O2 can be transported by hemoglobin? D D

  1. 1
  2. 2
  3. 3
  4. 4
  5. 5
48
Q

How many molecules of O2 can be transported by myoglobin? D D

  1. 1
  2. 2
  3. 3
  4. 4
  5. 5
49
Q

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
A

Thallassemia syndrome

50
Q

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
A

Homotropic effector

51
Q

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
A

All of the above

52
Q

what enzyme adds a phosphate group?

53
Q

What enzyme hydrolyzes peptide bonds?

A

Peptidases (Proteases)

54
Q

proteins that perform the same function but have different primary structures

55
Q

protein isoforms that function as enzymes

56
Q
  • Reservoir for oxygen
  • oxygen carrier that increases the rate of transport of oxygen within the muscle cell
57
Q
  • Transports oxygen from the lungs to the capillaries of tissues
  • It can also transport hydrogen and carbon dioxide from the tissues to the lungs
A

Hemoglobin

58
Q

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
A
  1. increased H+ (pH)
  2. Increased 2,3-bisphosphoglycerate
  3. Increased carbon dioxide
59
Q

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

60
Q

What are the markers of collagen that are not present in other proteins

  1. Glycine
  2. Hydroxyproline
  3. Hydroxylysine
  4. two of the options
A
  1. Hydroxyproline
  2. Hydroxylysine
61
Q

Where would you find Procollagen? D

  1. Golgi
  2. Rough Endoplasmic Reticulum
  3. Nucleus
  4. Extracellular Matrix
  5. Lysosomes
A

Rough Endoplasmic Reticulum

62
Q

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
A

Ehlers-Danlos syndeom (EDS)

63
Q

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

64
Q

RNAs with catalytic activity , much less encountered than protein catalysts

65
Q

enzyme that requires ATP

A

Synthetase

66
Q

Enzyme that does not require ATP

67
Q

Enzyme that removes a phosphate group

A

Phopshatase

68
Q

Enzyme that breaks bonds by using inorganic phosphate

A

Phyosphorlyase

69
Q

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

70
Q

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

71
Q

Enzyme that oxidizes a sub substrate by transferring oxygens to it

72
Q

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

A

Active site

73
Q

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

74
Q

Enzyme with its nonprotein component (active)

A

Holoenzyme

75
Q

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

76
Q

Nonprotein moeity (inorganic or organic) of the enzyme

77
Q

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

78
Q

Coenzymes that are permanently associated with the enzyme

A

Prosthetic group

79
Q

Coenzymes that are only transiently associated with the enzyme

A

Cosubstrate

80
Q

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
A

Allosteric Enzymes

81
Q

Which factors affect reaction velocity (speed of a reaction)

  1. Substrate concentration
  2. Temperatirs
  3. pH
  4. Acid/base
  5. three of the above
A

Increasing

  1. Substrate concentration
  2. Temperatirs
  3. pH
82
Q

What will reflect a low affinity of enzyme for the substrate

  1. Large Km
  2. Small Km
83
Q

What is related order of reaction with respect to the substrate when:

  • When [S] is much less than Km
  • V is proportional to [S]
A

First Order

84
Q

What is related order of reaction with respect to the substrate when:

  • When [S] is greater Km
  • V is constant and independent of [S]
A

Zero Order

85
Q

Any substance that can diminish the velocity of an enzyme-catalyzed reaction is called an

  1. Apoenzyme
  2. Inhibitor
  3. Holoenzyme
  4. coenzyme
86
Q

Reversible inhibitors typically bind to enzymes through

  1. covalent bonds
  2. hydrogen bonds
  3. noncovalent bonds
  4. Hydrophobic bonds
A

noncovalent bonds

87
Q

Irreversible inhibitors typically bind to enzymes through

  1. covalent bonds
  2. hydrogen bonds
  3. noncovalent bonds
  4. Hydrophobic bonds
A

covalent bonds

88
Q

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
A

Km increases, Vmax is unchanged and affinity decreases

89
Q

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
A

Km is unchanged, Vmax is decreases and affinity increases

90
Q

EffEffCE

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

Biomedical Sciences & Oral Ecosystems I (4 decks)

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