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Pharm 410: Fundamentals of Drug Action and Metabolism > Day 4: Protein structure > Flashcards

Day 4: Protein structure Flashcards

1
Q

What is the primary structure of a protein

A

Consists of a sequence of amino acids linked together by peptide bonds, and includes any disulfide bonds

All the amino acid residues

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2
Q

What is the secondary structure of a protein?

A

The resulting polypeptide chain from the primary structure can be arranged into untis, making the secondary structure, such as an alpha helix

The helix formed from the amino acid resiudes

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3
Q

What is the teriary structure of a protein?

A

The helix of the secondary structure is part of the tertiary structure of the folded polypeptide

the chain from the secondary structures folding together

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4
Q

What is the quaternary structure of a protein?

A

The folding of the polypeptides in the tertiary stucture make up subunits, which all of the subunits make up the final quaternary structure.

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5
Q

Whats a good way to think of the different types of structures of a protein?

A

The tertiary structure is like globe: contains all the features of the primary and secondary structures

The secondary structure is like a picture of the US: contains all the fearutres of primary structure

The primary structure would be like a picture of the hover dam: small and only contains one thing

The quaternary structure would be like the milky way: contains everything

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6
Q

What is a protein in terms of the AAs.

A

Each protein has a unique, precisley defined AA sequence predetermined by DNA (gene)

The amino acid sequence is often referred to as the primary structure. It includes disulfide bonds

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7
Q

Why is knowing AA sequences important?

A
  1. knowledge of the sequence of a protein is essential to understand MOA
  2. AA sequences determine three-dimensional structures of proteins
  3. alterations in AA sequence can produce severe and sometimes fatal diseases, such as dickel-cell anemia, cystic fibrosis, cancer
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8
Q

What can single AA mutations cause?

A

big changes in protein structure and function

RAS protein which changes and is the cause of 60-70% of various cancers

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9
Q

What does secondary structure describe?

A

The local conformation of the amino acids int he protein chain with two major secondary structures

  1. Alpha helix
  2. beta sheet
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10
Q

what are the two polypeptide segments without a distinctly folded arragement called? secondary structure

A

coil and turn

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11
Q

How is the alpha helix stabilized?

A

Its a coiled structure stabilized by intra-chain hydrogen bonds

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12
Q

How is a single polypeptide chain wound?

A

Its around an imaginary axis, with 3.6 amino acids per turn. The R-groups point outward

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13
Q

How do hydrogen bonds stablize a-helices?

A

There are hydrogen bonds between a carboxy-oxygen (partial negative charge) and the amino hydrogen (partial postive charge)

One amino acid forms hydrogen bond with the 4th amino acid further along the chain.

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14
Q

What does the a-helix provide?

A

Strength and toughness to the protein structure

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15
Q

What is the beta conformation of the polypeptide chains?

A

Its two or more extended strands of the polypeptide chain lie side by side (running parallel or antiparallel), help together by a regular array of hydrogen bonds bwteen backbone NG and C=O groups, to form a ridged planar surface

drawn as a broad arrow

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16
Q

Why is proline not found in alpha helix or beta sheet structure?

A

Proline does not have amino group instead it has imino group. which produces destabilizing kink and interferes with hydrogon bonding

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17
Q

Why is glycine extremely rare within the alpha helix and beta sheet structure?

A

due to lack of R-group, its much more flexable. if its in the structure it introduces weakness in the cylindrical feature or constrained beta sheet structure.

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18
Q

What are turns in secondary structure?

A
  1. 180 degress are important for the bend between the different strands of antiparallel b-sheets
  2. contain roughly 4 amino acid residues
  3. often contain glycine for flexibility and proline for kink or bend
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19
Q

what are coils in secondary structure

A
  1. include any structure other than those mentinoned above
  2. they have important function: add fexibility to the protein and allow for confromational changes
  3. glycine and prolien are frequently present
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20
Q

what are the ways of drawing polypeotide structures?

A

Polypeptide threads become ribbons in areas of alpha (green) and beta (red) folded secondary structure.

In beta sheet cartoons, arrows on the ribbons show the direction of the amino acid sequence, going from the amine-terminus toward the carboxy-terminus

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21
Q

What are prion diseases or transmissible spongiform encephalopathy (TSE)?

A

Secondary structure alteration

family of progressive neurodegenerative disorder that affect both humans and animals

Myriads of small holes develop in the brain to attain a sponge like structure

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22
Q

What are the causes of prion diseases or transmissible spongiform encephalopathy (TSE)

A

Misfoled prions

Prions = abnormal cellular proteins that are tansmissible and are able to induce abnormal folding of specific normal cellular proteins

mostly happens in the brain

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23
Q

What is the difference between diseased and normal prions?

A

Both have same primary structure (same amino acid sequence) but the diseased prion is more stiff, tends to aggregate and has limited resistance to digestion by proteases

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24
Q

What is the tertiary structure in terms of 3-dimensional arrangment?

A

Its the 3-dimensional arrangement of the secondary structural elements within a folded protein.

The overall course of a single polypeptide chain (product of a single gene) of a protein is referred to as itss tertiary structure

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25
Q

what is the globular proteins of tertiary structure?

A

Compact, highly-folded proteins that are water-soluble

Myoglobin

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26
Q

what are fibrous proteins tertiary structure?

A

stiff, elongated proteins that tend to form insoluble fibers

Collagen

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27
Q

What is a globular protein when it comes to being hydrophilic and hydrophobic?

A

The surfaces of globular proteins AA residues interact with water, hence those are hydrophillic

Hydrophobic AAs frequently remian in the core of globular proteins

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28
Q

What is scurvy?

A

Prolonged vitamin C deficiency leads to loss of collagen quaternary structure, leads to bleeding gums, loose teeth, skin lesions, weakned blood vessel walls (bruising), and poor would healing

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29
Q

What is protein folding (teriary structure) is driven primarly by?

A
  1. Hydrophobic effect (non-plar resides face in; polar face out)
  2. electrostatics ( dipoles, H-bonding, ion pairing/salt bridges)
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30
Q

What causes proteins to be denatured?

A
  1. heat
  2. Mechanical agitation - molecular motion
  3. pH - ion and H-bonding disruption
  4. Detergents - hydrophobic disruption
  5. Organic solvents - (acetone, alcohols) hydrophobic disruption
  6. chaotropic agents (probably means “chaos-causing”)
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31
Q

What is the term protein denaturation almost always associated with

A

globular proteins since almost all biologically actice proteins are globular and soluble

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32
Q

Whats an easy way to determine protein denaturation

A

Precipitation

Looks like clumps are formed and gets cloudy

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33
Q

What does it mean when a protein is renatured?

A

Returing to the original functional folded conformation. This occurs by removing the denaturant and placing the protein in the conditions where its native conformation is favored

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34
Q

What does it mean if a protein is permanently denatured?

A

Usualy under various conditions (high heat, harsh treatment) cant be renatured anymore, like egg white when heated

35
Q

Since O2 is poorly soluble how does hemoglobin help transport it?

A

Hemoglobin is an oxygen transporter its necessary to carry oxygen to cells and tissues, especially those that are distant from the lungs

hemoglobin increases the availability of O2 in our body seventy times

36
Q

Where is myoglobin and hemoglobin found?

A

Myoglobin - found in muscle cells, for O2 storage

Hemoglobin - found in red blood cells, for O2 transport to tissue

37
Q

How is heme used to bind O2?

A

Heme is considered a prosthetic group: one type of co-factor, a non-protein component that is premanently attatched to a protein and is required for protein function.

heme is attached to both myoglobin and hemoglobin

38
Q

What is an Apoprotein

A

The polypeptide part of a conjugated protein

39
Q

What is a Holoprotein?

A

The complete, biologically acticce protein conjugate, consisting of the folded polyoeotude chain(s) and any relevant prosthetic groups or cofactors

40
Q

How is myoglobin as a marker of acute MI?

A

Myoglobin is found in a high concentration in both cardiac and skeletal muscle

Its released into serum as early as 1 hour after AMI

Reaches peak in the range of 4 to 12 hours, then rapidly cleared

Myoglobin is released eailer from dmged cells than other cardiac markers, allowing for earlier detection of AMI

Not used by hospitals because its poor clinical specificity, owing to the presence of large quantities of myoglobin in skeletal muscule

Myoglobin, potentially useful for ruling out, but not for confirming diagnosis of AMI

41
Q

How does Heme work with Fe2+

A

Fe2+ ion is contained in the center of a large heterocyclic organic ring called a porphyrin. Oxygen binds to the Fe2, the color of heme as well as hemoglobin changes depending on the conjugation partner.

42
Q

What is the color of O2 bound to Fe2+

A

bright red

43
Q

What is the color of CO2 bound to hemoglobin

A

Dark red

44
Q

What is O2 not bound to Fe2+

A

blue

45
Q

What are the three properties that regulate oxygen release from hemoglobin?

A
  1. cooperative nature of hemoglobin (local)
  2. 2-3 BPG increases oxygen dissociation (systemic)
  3. CO2 inc, and pH down, oxygen dissociation up - bohr effect (local)
46
Q

What is hemoglobin cooperative binding?

A

The first O2 binding triggers conformational change to other subunits, which makes O2 binding much stronger and easier for other subunits

47
Q

Does Hemoglobin retain most oxygen?

A

Yes, even after releasing O2 to the tissues, total Hb remains 60-70% oxygentated

This reserve is useful for exercising muslce AND sufficient to maintain life for several minutes following acute respiratory arrest

48
Q

what is 2,3-BPG (2,3-bisphosphoglycerate)

A

a derivative of glucose metabolism. it is a potent modifier of hemoglobin binding affinity

2,3-BPG binds to the T-conformation of Hb to b-subunits in the center of the complex: this reduces the oxygen affinity of hemoglobin

49
Q

How does 2,3-BPG modulation helps body adapt to low pO2?

A

at sea level hemoglobin is nearly 100% saturated with O2 in lungs: after going to tissues hemoglobin; the hemoglobin coming back to the lungs is around 60% saturated. 40% of O2 is relased in tissue

In high altitudes O2 in air is low. As a result homoglobin is 70% saturated in the lungs. This means that hemoglobin can only supply about 10% oxygen to tissues

In this situation 2,3-BPG concentration increases in the body, as a result hemoglobin affinity to oxygen decreases and more oxygen is relased

50
Q

What is the Bohr effect?

A

As pH decreases due to the increased production of CO2, so does the affinity of hemoglobin for O2

Metabolically active tissues produces more CO2 as a result the environment becomes more acidic. CO2 reacts with water to form carbonic acid

With the lower pH, H+ binds to hemoglobin, which relases O2 from the hemoglobin

The same is true when pH is higher with a decrease in CO2 results in hemoglobin picking up more oxygen

51
Q

What is homotropic and positive cooperativity

A

binding of the ligand to a specific ligand binding site on one subunit increases the affinity of the other subunits for the same ligand

EX: hemoglobin and oxygen (ligand)

52
Q

What is heterotropic and negative cooperativity?

A

When ligands are different and affinity is decreased

EX: ligands such as CO2, H+ and 2,3-BPG negativley affect the affinity of the binding sites in Hb for O2

53
Q

How does the number for partial oxygen pressure (pO2) work?

A

the lower the number the higher the demand for oxygen

the lungs have a pO2 of 100mm Hg whereas tissues have 40 mm Hg

54
Q

What is carbamino hemoglobin?

A

When CO2 becomes non-enzymatically bound to the amino terminus of Hb subunit.

it transport CO2 away from tissues and back to the lungs to be exhaled

55
Q

How is most of the CO2 in the blood exist?

A

90% is in the form of bicarbonate ion (HCO3-)

the rest of the CO2 remains as dissolved CO2 gas

56
Q

What is Immunoglobulin G? (IgG)

A

Major class of antibody molecule and one of the most abundant proteins in the blood serum

57
Q

What does Immunoglobulin (IgG) have in terms of polypeptide chains?

A

It has 4 polypeptide chains: two larges ones, called heavy chains (50kDa), and two light chains (25kDa)

58
Q

What is a pregnancy test and how does it work?

A

designed to tell if your urine or blood contains a hormone called human chorionic gonadotropin (hCG). this hormone is made right after a fertilized egg attches to the wall of a womans uterus

Usually happens about 6 days after fertilization. during pregnancy, levels of hCG continue to rise, doubling every 2-3 days

59
Q

What is actin?

A

A globular protein. Two actin fibers coil to make the thin filament core

part of a muscle

60
Q

What is tropomyosin?

A

Fibrous protein. containing two a-helices coiled around each other. Tropomyosin polymerizes end-toend and threads along the thin filament groove formed by the coiled actin strands

61
Q

What is troponin?

A

A regulatory complex of 3 globular protein subunits. The 3 subuniuts are designated troponin C (the calcium-binding component), TnT (the tropomyosin-binding component), and TnI (the inhibitory component)

62
Q

What is thick filament composed of?

A

Multimeric protein Myosin

Has 4 heads and those myosin head regions bind to actin and ATP

63
Q

What is a point mutation?

A

A single AA is changed

Leads to RAS cancer

64
Q

Whats important to remember what the primary structer contains?

A

Cross linking with disulfide bonds

65
Q

How does an alpha helix sabilize itself?

A

Using hydrogen bonding between AA within the stucture

66
Q

What are the charaterics of proteins secondary structure?

A

Alpha helix, beta sheets are primary but can also have coils or turns

67
Q

How many amino acids are involved in a single polypeptide chain?

A

3.6 amino acids

68
Q

How are parallel and antiparallel B-sheets aligined?

A

Parallel - the N and C termals are lined up on each side

Antiparallel - N and C are mixed together

69
Q

What is something A- helixes and B-sheets have in common?

A

They will be missing proline

70
Q

What is transmissible spongiform encephalopathy?

A

TSE, its prion diseases in the brain, misfoled prions

CJD (creytzfeldt-jakob disease)

BSE (maad cow disease)

71
Q

What is tertiary structure?

A

Its 3-dimensionla arrngemtn of secondary structure

72
Q

Whats are globular proteins?

A

They are highly foled and WATER-SOLUBLE!!!

works in aqueous solution enzyme in blood

73
Q

What are fibrous proteins

A

Stiff, elongated INSOLUBLE FIBERS

74
Q

In globular proteins where would an nonpolar amino acid be located such as valine?

A

On the inside of the protein !

75
Q

Pt comes into hosptial compains of chest pain and his myoglobin is normal, do you think they had a heart attack?

A

No, myoglobin shows up with any type of muscle dmg within 1 hour, so if he doesnt have increased myglobin its likey they dont have a heart attack

76
Q

When do symptoms of Carbonmonoxide start to show up?

A

7% saturation

77
Q

What percent of saturation of carbonmonoxide will cause death?

A

25%

78
Q

What saturation does hemoglobin have with carbonmonoxide of smokers?

A

4-8%

79
Q

How much saturation does hemoglobin keep after releasing O2 tissues?

A

60-70%

80
Q

Where does 2,3, BPG bind?

A

at the t-conformation of hb to Beta subunits

81
Q

Does 2,3 BPG affect HbF

A

No, HbF does not have beta chains so it can not bind it

82
Q

What causes sickle cell anemia?

A

A point mutation in the beta globin gene. As a result a valine (non-polar amino acid) is inserted into the B-globin chain instead of glutamic acid (charged polar amino acid) this causes it to be more hydrophobic

83
Q

What is the one good thing that comes from people with sickle cell

A

They are ristant to malaria

Pharm 410: Fundamentals of Drug Action and Metabolism (8 decks)

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