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Biochemistry > Chapter 2- Proteins > Flashcards

Chapter 2- Proteins Flashcards

1
Q

Functions of proteins (6)

A
  1. Biological catalysts- production of ATP, etc
  2. Protein transport- hemoglobin transports oxygen, and proteins act as channels in the cell membrane
  3. Structure- make up cytoskeleton
  4. Mobility- sperm cells have a flagellum
  5. Immunity- antibodies and antigens
  6. Communication- peptide hormones are involved in intracellular and intercellular communication
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2
Q

How many amino acids are there?

A

20

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3
Q

Functional groups

A

Amino acids within proteins have different functional groups. Different functional groups have different capabilities and reactivities. The arrangement and sequence of functional groups determines the protein’s function- this is important for enzymes

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4
Q

What encodes proteins?

A

Proteins are encoded by DNA. Cells use DNA to create RNA, then ribosomes use the RNA to create proteins

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5
Q

Alpha carbon

A

A central carbon attached to the carbonyl group (deprotonated carboxylic acid, COO-), protonated amino group (NH3), and an R group

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6
Q

Chirality

A

Chiral carbons have 4 different groups attached to them. Can have an R or S configuration

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7
Q

Which configuration (R or S) is most prevalent?

A

18 out of the 19 chiral amino acids exist their in S absolute configuration form. Only cysteine exists in the R configuration

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8
Q

How to determine chirality configuration

A

To determine the configuration, each group gets a number of priority (1-4). The group that gets number 1 has the highest atomic number. H is always given a 4, the amino group is almost always given a 1 since nitrogen has the higher atomic number. The 4 group (H) should be on a dashed line. Draw an arrow from 1 to 3- counterclockwise= S configuration, clockwise= R configuration

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9
Q

What determines whether the amino group and carboxylic acid group are protonated or deprotonated?

A

The pH of the solution the amino acid is in

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10
Q

Dipolar/zwitterion form

A

In this form, the amino group is protonated and has a positive charge, while the carboxylic acid group is deprotonated and has a negative charge. This creates a polar species- we have 2 dipole moments. Dipolar form tends to exist at a pH of about 4-7. Also called an ionization state.

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11
Q

At low pH, how is an amino acid typically protonated?

A

At a low pH of about 1, the amino group remains positive but the carboxylic acid group is protonated and no longer has a charge. Results in a positively charged species. At a pH of about 2, the hydrogen on the COOH group begins to dissociate

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12
Q

At a high pH, how is an amino acid usually protonated?

A

At a pH of about 9, the amino group is deprotonated, resulting in a neutral charge. The carboxylic acid group is still deprotonated, resulting in a negatively charged species

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13
Q

Side chains are distinct from each other based on (6)

A
  1. Size
  2. Polarity
  3. Shape and structure
  4. Charge
  5. Hydrophobic properties
  6. Ability to hydrogen bond
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14
Q

8 amino acids with nonpolar/nonreactive side chains

A
  1. Alanine (Alo, A)
  2. Valine (Val, V)
  3. Leucine (Leu, L)
  4. Isoleucine (Ile, I)
  5. Methionine (Met, M)
  6. Phenylalanine (Phr, F)
  7. Tyrosine (Tyr, Y)
  8. Tryptophan (Trp, W)
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15
Q

Alanine

A

Alo, A. The side chain of A is made up of hydrocarbon molecules, so it’s nonpolar. This side chain is the smallest hydrocarbon side chain.

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16
Q

Valine

A

Val, V. Hydrocarbon side chain that is hydrophobic

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17
Q

Leucine

A

Leu, L. Hydrocarbon side chain that is nonpolar

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18
Q

Isoleucine

A

Ile, I. Hydrocarbon side chain that is hydrophobic. This is the largest hydrophobic side chain, so it’s most hydrophobic

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19
Q

Methionine

A

Met, M. M has a sulfur molecule in its side chain. Sulfur is about the same electronegativity as carbon, which is why this bond is also nonpolar, non reactive, and hydrophobic.

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20
Q

Phenylalanine

A

Phr, F. Has rings in its side chain. The F side chain contains a benzene ring, which only contains carbon and hydrogen. Makes the side chain very hydrophobic and non reactive.

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21
Q

Tyrosine

A

Tyr, Y. Has a ring in its side chain and has an electronegative oxygen. Y (and W) are slightly less hydrophobic due to the electronegative atoms. The ring structures still make the amino acids hydrophobic

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22
Q

Tryptophan

A

Trp, W. Has a ring in its side chain (indole) and has an electronegative oxygen. W (and Y) are slightly less hydrophobic due to the electronegative atoms. The ring structures still make the amino acids hydrophobic

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23
Q

How does the hydrophobic effect influence amino acid structure?

A

Hydrophobic side chains of the amino acids tend to pack together rather than interact with water- the side chains will point into the protein structure. Hydrophilic side chains will be found on the outside of the protein.

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24
Q

Amino acids with polar side chains (5)

A
  1. Serine (Ser, S)
  2. Threonine (Thr, T)
  3. Asparagine (Asn, N)
  4. Glutamine (Gln, Q)
  5. Cysteine (Cys, C)
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25
Q

Serine

A

Ser, S. Side chain has a hydroxyl group attached to the carbon. Oxygen is much more electronegative than hydrogen and has a partial negative charge, creating a dipole moment- polar side chain.

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26
Q

L isomer

A

When 4 different groups are bonded to the alpha carbon, the protein is considered chiral and can therefore exist as 2 mirror image forms (L isomer and D isomer). Only the L isomer exists in proteins.

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27
Q

Threonine

A

Thr, T. Carbon in the side chain contains a methyl, so the carbon is chiral. Also has a hydroxyl group which creates a dipole moment- polar side chain.

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28
Q

Asparagine

A

Asn, N. Double bonded oxygen is partially negative- carbon it’s bonded to is partially positive, and nitrogen is partially negative. Side chain is polar and much more reactive than the hydrophobic side chains

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29
Q

Glutamine

A

Gln, Q. Very similar to N, just has an extra CH2 group. Double bonded oxygen is partially negative- carbon it’s bonded to is partially positive, and nitrogen is partially negative. Side chain is polar and much more reactive than the hydrophobic side chains

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30
Q

Cysteine

A

Cys, C. Similar to S, but the oxygen is replaced with a sulfur. Known as a special amino acid due to its importance in forming disulfide bridges

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31
Q

Amino acids with special side chains (2)

A
  1. Glycine (Gly, G)

2. Proline (Pro, P)

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32
Q

Glycine

A

Gly, G. Smallest amino acid and also achiral- the side chain is only an H atom- doesn’t have an enantiomer. Doesn’t have any CH2 groups so it can’t be labeled as hydrophobic, but can interact with hydrophobic or hydrophilic side chains due to its small size

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33
Q

Proline

A

Pro, P. Technically hydrophobic. Has a special structure due to the 5 membered ring shape- this is the only side chain that connects to the alpha carbon and to the nitrogen. The 5 membered ring makes it structurally restrictive- it influences the structures of special types of proteins

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34
Q

What charge do basic amino acids have?

A

positive charge at physiological pH

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35
Q

Basic amino acids (3)

A
  1. Lysine (Lys, K)
  2. Arginine (Arg, R)
  3. Histidine (His, H)
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36
Q

Lysine

A

Lys, K. Long side chain (4 carbons) with an amino group. The full positive charge on the amino nitrogen gives the molecule a net positive charge- positive charge makes the amino acid basic

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37
Q

Arginine

A

Arg, R. Long side chain- 3 carbons, then an NH, then another carbon that’s bonded to 2 amino groups. The terminal portion is called a guanidinium group, which is positively charged at neutral pH. The positive charge is delocalized due to the resonance stabilization of guanidinium

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38
Q

Histidine

A

His, H. Can exist in a protonated or deprotonated state at neutral pH, since its pKa (6) is near physiological pH. The ring on the histidine side chain is called an imidazole group- this is an aromatic ring that can stabilize charges by resonance. The nitrogen on the ring can be protonated, creating a positive charge

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39
Q

What charge do acidic amino acids have?

A

Have negative charge at physiological pH- at above a pKa of 4.1, these amino acids are likely to exist in their deprotonated state.

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40
Q

Acidic amino acids (2)

A
  1. Aspartate (Asp, D)

2. Glutamate (Glu, E)

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41
Q

Aspartate

A

Asp, D. At a low pH, the carboxylate ion group is protonated. The amino acid is then called aspartic acid.

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42
Q

Glutamate

A

Glu, E. Side chain has one additional carbon compared to D. Like D, E contains a negatively charged carboxylate group at the normal physiological pH. At low pH, the carboxylate group is protonated, removing the negative charge and glutamic acid

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43
Q

How many amino acids have ionizable side chains?

A

7

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44
Q

What does “readily ionizable” mean in regard to amino acids?

A

This means that at certain pH values, the ionizable side chains will be able to exchange hydrogen atoms (can donate or accept H atoms). It gives them the ability to participate in acid-base reactions and to form ionic bonds with other macromolecules- makes these 7 amino acids reactive and lets them participate in many different biological reactions

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45
Q

Readily ionizable amino acids (7)

A
  1. Aspartic acid
  2. Glutamic acid
  3. Histidine
  4. Cysteine
  5. Lysine
  6. Tyrosine
  7. Arginine
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46
Q

Why are aspartic and glutamic acid ionizable?

A

both of these have a side chain group with a carboxylic acid

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47
Q

Why is histidine ionizable?

A

pKa= 6, so very close to physiological pH. The H that binds to nitrogen can be frequently exchanged (added or removed). Therefore, histidine switches between forms

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48
Q

Why is cysteine ionizable?

A

pKa= 8.3, so the sulfur of the amino acid is acidic 50% of the time and basic (negatively charged) 50% of the time

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49
Q

Why is tyrosine ionizable?

A

Has a neutral, nonpolar side chain (OH). The side chain is also hydrophobic, and will be found inside of the protein structure

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50
Q

Why are lysine and arginine ionizable?

A

Have a polar hydrophilic side chains that are positively charged- these side chains can form ionic bonds

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51
Q

If the pH of the amino acid is above the pKa, which form predominates?

A

The conjugate base form. This is why at a pH of 7, all amino acids have the alpha carbonyl group in conjugate base form- oxygen is negatively charged

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52
Q

Peptide bond

A

A peptide bond is a type of covalent bond that holds amino acids together. Can occur between the carbon on one amino acid and the nitrogen on another

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53
Q

Why did these 20 amino acids become the ones to make up all proteins? (3 possibilities)

A
  1. These amino acids provide chemical versatility
  2. They may have been available for prebiotic reactions
  3. Larger amino acids may be too reactive
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54
Q

Dehydrolysis/condensation reaction

A

When forming a peptide bond, one water molecule is released- one oxygen and two hydrogens are removed when the amino acids react

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55
Q

Hydrolysis

A

When a bond breaks using a water molecule

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56
Q

Why does the formation of a peptide bond require ATP?

A

The bond requires energy since the reaction is thermodynamically unfavorable (reactants are more thermodynamically stable than products).

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57
Q

Why don’t peptide bonds break spontaneously?

A

The reaction requires a high activation energy. Therefore, it would be thermodynamically favorable for a peptide bond to break, but it would not be kinetically favorable since more energy is needed to break the bond- it’s too high to occur under normal conditions

58
Q

What is considered the beginning of the polypeptide chain?

A

The end with the amino terminal residue (NH3 sticking off). All amino acids have directionality/polarity.

59
Q

Primary structure definition

A

The specific sequence of amino acids in the polypeptide chain

60
Q

Residue

A

Each amino acid in a polypeptide chain

61
Q

Backbone

A

The repeating nitrogen-carbon-carbon pattern making up the main chain of atoms. The polypeptide chain as a whole has a potential to form a hydrogen bond with other molecules

62
Q

Why does the backbone have hydrogen bonding potential?

A

The hydrogen bond donor is an N-H group

The hydrogen bond acceptor is a C=O group

63
Q

Why do peptide bonds have double bond character?

A

Because they are resonance stabilized. For example, the lone pair on the nitrogen can form a double bond and the oxygen’s double bond can move to give oxygen a negative charge, making the peptide bond between carbon and nitrogen a double bond. Single bonds can rotate, double bonds can’t. Therefore, peptide bonds can’t rotate since they have double bond character.

64
Q

What characteristics does double bond character give a peptide bond (3)

A
  1. Makes the peptide bond planar
  2. Prevents any rotation about the peptide bond
  3. The peptide bond is uncharged
65
Q

Why is the trans configuration of a peptide bond more stable?

A

The trans configuration of a peptide bond is thermodynamically more stable and lower in energy than the cis configuration. With the trans configuration, the alpha carbons on either side of the peptide bonds point in opposite directions. Since the groups point away from each other, there will be no steric hindrance- no electrostatic repulsion or atom/electrons getting in the way

66
Q

ɸ (phi) angle of rotation

A

The angle of rotation between the nitrogen and the alpha carbon atom of an amino acid

67
Q

Ѱ (psi) angle of rotation

A

The angle of rotation about the single bond between the alpha carbon and the carbonyl carbon atom

68
Q

What is the significance of the phi and psi angles of rotation?

A

These rotations allow the protein to fold into its 3D structures- not all of these rotations are possible due to steric hindrance. The bonds the rotations occur in are not peptide bonds. Therefore, they are not resonance stabilized and are able to rotate

69
Q

Secondary structures (4)

A
  1. Alpha helices
  2. Beta pleated sheets
  3. Beta turns
  4. Omega loops
70
Q

Which bonds rotate to form a secondary structure?

A

The rotation of the single bonds inside the polypeptide (not the peptide bonds) occurs to form the secondary structure- bonds between the NH and CO groups coming off of the alpha carbon

71
Q

Most proteins consist of how many amino acids?

A

50-2,000

72
Q

The average molecular mass for an amino acid is

A

110 g mol ^ -1

73
Q

Why is it important to know amino acid sequences?

A
  1. Amino acid sequences determine the 3D structure of proteins
  2. Alterations in amino acid sequence can lead to abnormal protein function and disease
  3. The sequence of a protein can reveal a lot about its evolutionary history
74
Q

How does proline’s structure influence the peptide bond?

A

When proline follows another amino acid, the peptide bond between them is equally likely to be in cis or trans form due to proline’s unusual geometry

75
Q

Torsion angle

A

Rotation about the psi and phi bonds- determines the path of the polypeptide chain. Not all torsion angles are allowed.

76
Q

Ramachandran plot

A

Illustrates the psi and phi angles that are favorable because there is no steric hindrance.

77
Q

Secondary structure

A

The 3D structure formed by hydrogen bonds between peptide NH and CO groups of amino acids that are near one another in the primary structure.

78
Q

Alpha helix

A

Formed when the polypeptide chain twists to form a rod-like structure. The backbone is located on the inner part of the helix and the side chains are on the outer part. Each amino acid uses its NH group to form a hydrogen bond with the CO group of the amino acid that is 4 units ahead of it

79
Q

Screw sense of an alpha helix

A

The screw sense of an alpha helix is the direction in which the helix rotates with respect to its axis- to figure this out, start from the bottom end of the helix and trace the path going up
If horizontal, you can start from either side

80
Q

Right handed alpha helix

A

Rotates clockwise, predominates due to less steric hindrance

81
Q

Left handed alpha helix

A

Rotates counterclockwise, less stable because there’s more steric hindrance- the left handed helix has a higher energy level

82
Q

Beta sheets

A

Linear, polypeptides are stacked on top of each other. Can be parallel or antiparallel.

83
Q

Anti parallel beta sheet

A

The sheets point in opposite directions. The NH and CO groups of an amino acid on one strand form hydrogen bonds with the CO and NH groups of the opposing amino acid on the other strand. There is a one-to-one connection between each group, so the polypeptides line up perfectly

84
Q

Parallel beta sheet

A

The sheets point in the same direction. An amino acid on one strand connects to two amino acids on the opposing end via hydrogen bonds- the polypeptides do not line up perfectly. On one amino acid, the NH group and CO group bond to one CO group on one amino acid and one NH group on a separate amino acid

85
Q

The compact nature of proteins is caused by

A

The polypeptide’s ability to make sudden turns in their chain. These turns, called beta turns or reverse turns, are stabilized by hydrogen bonding. Can also make omega loops. They allow the polypeptide to make abrupt turns and are usually found on the surface of the protein. A bond forms between the CO group and the H on the NH group on another amino acid

86
Q

Tertiary structure definition

A

The spatial arrangement of amino acids that are found far away from one another along the polypeptide chain.

87
Q

Which factor is most important for establishing tertiary structure?

A

Hydrophobic interactions are most important- this is because protein interactions are taking place with water as the solvent. Most proteins exist in aqueous solution. We know that when non-polar molecules are placed into water, they will aggregate together because this will create a thermodynamically more stable system (hydrophobic effect)

88
Q

Myoglobin

A

An example of a protein that is highly compact, globular, and mainly helical, with a heme prosthetic group

89
Q

When a tertiary structure is folding, how will amino acids rearrange themselves?

A

We have many different types of side chains- some are polar and hydrophilic, others are hydrophobic. Those amino acids with hydrophobic side chains- valine, leucine, and others- will tend to be found inside the protein. Amino acids with hydrophilic side chains- lysine, aspartate, and others- tend to be found on the outside of the protein.

90
Q

In a tertiary structure, how will the nonpolar amino acids interact with each other?

A

The nonpolar amino acids of the protein core interact with one another through instantaneous dipole moments (van der waals forces). These forces are weak on an individual basis, but the aggregate effect of the many nonpolar amino acids creates a substantial binding effect

91
Q

How are amino acids distributed in a membrane embedded protein?

A

These proteins have many hydrophobic amino acids in contact with the hydrophobic membrane and many polar and charged amino acids in contact with the polar substance it is assisting across the membrane.

92
Q

Disulfide bridges

A

if two cysteine amino acids are in close proximity and an oxidation reaction takes place, a covalent bond can be formed between the sulfur groups of the molecules (hydrogens are removed). In some proteins, usually the ones destined to be extracellular, the polypeptide chains can be cross linked via disulfide bonds between cysteine residues. These cross linked units are called cysteines.

93
Q

Ionic interactions

A

Two oppositely charged side chains can interact with ionic bonds. For example, lysine (positive charge on the side chain) can form an ionic bond with aspartate (negative charge on the side chain)

94
Q

Motifs

A

Supersecondary structures of a protein. They are common combinations of secondary structure that are present in many proteins and frequently exhibit similar functions. For example, a helix-turn-helix motif is common in DNA binding proteins.

95
Q

Domains

A

Independently folding regions within a polypeptide, connected by a short, flexible linker segment

96
Q

Coiled-coil proteins examples (3)

A
  1. Alpha keratin
  2. Cytoskeletal proteins
  3. Muscle proteins
97
Q

Coiled-coil proteins

A

Two right handed alpha helices intertwine to form a left handed super helix stabilized by ionic and van der waals interactions. These proteins are strong and flexible due to their intertwining coil design

98
Q

Collagen function

A

Structural protein in skin, bone, tendons, cartilage, and teeth

99
Q

Collagen structure

A

Consists of 3 intertwined helical polypeptide chains, which form a superhelical cable. The polypeptide chains are not alpha helices, and they are stabilized by steric repulsion of the proline rings. The chains interact through hydrogen bonds. The interior of the superhelical cable is crowded- only glycine can fit inside.

100
Q

Collagen single strand conformation

A

Glycine appears at every third residue, and the sequences gly-pro-hyp and gly-pro-pro are common, where hyp is a hydroxylated proline.

101
Q

Collagen defects

A

Collagen defects cause disease. Osteogenesis imperfecta (brittle bone disease) occurs if a mutation results in the substitution of another amino acid in place of glycine.

102
Q

Quaternary structure

A

In some cases, large proteins can actually consist of two or more polypeptide chains- quaternary structure refers to the ways in which these two or more polypeptides interact with one another

103
Q

Subunit

A

Each individual polypeptide chain in a quaternary structure. The subunits can be identical or different depending on the protein

104
Q

Dimer

A

The simplest case of quaternary structure. In a dimer, there are two polypeptides that constitute the protein. We can also have triamer (3 subunits), tetramer (4 subunits), and so on

105
Q

How are subunits of quaternary structures usually held together?

A

These subunits are usually held together by non-covalent bonds but can also be held together by covalent bonds such as disulfide bridges.

106
Q

Major categories of quaternary structure (2)

A
  1. Fibrous proteins

2. Globular proteins

107
Q

Examples of fibrous proteins

A
  1. Collagen is found in connective tissue, like bone

2. Keratin is found in hair or nails

108
Q

Alpha keratin

A

The main component of hair and it consists of two polypeptide subunits. These subunits consist of right-handed alpha helices that intertwine to form a left-handed supercoil called the alpha coiled coil. This is a dimer since it consists of 2 subunits

109
Q

The 2 subunits of alpha keratin are held together by (3)

A
  1. Van der Waals forces- between nonpolar side chains of amino acids
  2. Ionic bonds- between negatively charged and positively charged side chains
  3. Disulfide bonds- covalent bonds between 2 adjacent cysteine amino acids
110
Q

The more disulfide bonds we have

A

The more rigid the protein will be

111
Q

Globular protein examples (3)

A

These proteins have a wide range of functions and are relatively spherical in shape. Some examples include:

  1. Hormones- insulin is a globular protein
  2. Enzymes- DNA polymerase, allows replication of DNA during mitosis and meiosis
  3. Hemoglobin
112
Q

Hemoglobin

A

Hemoglobin is a tetramer that consists of 4 individual subunits. Picks up oxygen in the lungs, brings it to tissues in the blood. Each subunit is equipped with a heme group that is capable of binding an oxygen molecule- we can bind 4 oxygen per hemoglobin molecule. Slight changes in hemoglobin structure can change its affinity to oxygen

113
Q

Do all proteins have quaternary structure?

A

No. For example, myoglobin is a protein that carries oxygen in the muscle. It only has tertiary structure, and only one single polypeptide chain.

114
Q

Anfinsen experiment of protein folding

A

Series of experiments that ultimately showed that the information needed to form the 3D active protein lies in its sequence of amino acids.

115
Q

Which enzyme did Anfinsen study?

A

Ribonuclease- catalyzes the breaking down of RNA molecules in the cells and has a tertiary structure. The plan was to destroy the tertiary and secondary structure of ribonuclease by using appropriate agents and then investigate the conditions under which the proper tertiary structure was reformed.

116
Q

Prions

A

Prions are infectious agents that consist entirely of protein aggregates. The aggregates are insoluble, so our cells can’t break them down or denature them. These agents are responsible for mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease (CJD) in humans.

117
Q

3 characteristics of prions

A
  1. Aggregates of protein that are normally present in the body that misfold
  2. Transmissible- prions can also act as infectious agents- transmitted from beef of infected cows to humans
  3. Generally cannot be broken down or denatured by typical methods
118
Q

What happened in Anfinsen’s experiment when the denaturing agents were removed?

A

The enzyme regained its original structure and reactivity

119
Q

First step in Anfinsen’s experiment

A

The first step was to fully unfold the protein- beta mercaptoethanol was used to break the covalent disulfide bonds

120
Q

Denaturation of ribonuclease requires which 2 reagents?

A
  1. Beta mercaptoethanol reduces disulfide linkages

2. Urea disrupts noncovalent interactions

121
Q

In Anfinsen’s experiment, how was correct disulfide bond pairing established when the reagent was removed?

A

To regain enzyme activity, urea must be removed and a trace of beta-mercaptoethanol must be present. This allows the slow formation and breakage of disulfide bonds over the course of several hours, until the lowest energy and most stable active form is regenerated.

122
Q

How is a misfolded protein different from a regular protein?

A

For example, PrP is a normal protein found in the brain. Under certain conditions, they can misfold into protein PrPSC. Notice that the misfolded protein has a much greater content of beta pleated sheets than the normal protein. This means that some of the alpha helices are converted into beta sheets.

123
Q

How can a greater amount of beta pleated sheets in a protein cause aggregation?

A

Beta pleated sheets have a high propensity for forming bonds with other beta pleated sheets. Therefore, the beta sheets of one protein can bond to the beta sheets of another one, forming aggregates. Use noncovalent bonds. The beta pleated sheets bond to form an aggregate of multiple pleated sheets, and they are able to somehow transform normal proteins into an even larger PrPSC aggregate (amyloid fiber). The larger and larger aggregates will interfere with normal cellular functions, eventually resulting in the death of those cells. The mechanism for how this happens is unclear.

124
Q

How does the denaturing of a protein progress?

A

At normal temperature and with no denaturing agents, 0% of the protein is denatured. As the temperature or the amount of denaturing agent increases, you eventually get to a point where the amount of protein that is denatured increases drastically. Once the denaturing agent is removed or the temperature goes back to normal, the primary structure of the protein dictates the refolding process and the polypeptide reforms it native conformation. This is due to the cooperative folding of proteins

125
Q

Protein cooperative folding curve

A

Starts off with a slightly positive slope, then sharp positive slope, then the line is mostly horizontal (no slope).

126
Q

Cooperative protein folding

A

Under some denaturing condition, a segment of a protein becomes unstable and begins to break down. As that segment denatures, it causes disruptions in other segments of the polypeptide. As other segments are disrupted, they begin to break down also- this is the reason for the sharp increase on the graph. In this sense, the many segments of the protein cooperate to break down the overall structure of the protein. The reverse is also true.

127
Q

When proteins are folding or unfolding, which intermediate states do they go through? (4)

A
  1. Native state- tertiary structure, where amino acids that were far apart from each other in the polypeptide chain are interacting.
  2. Intermediate state A- noncovalent interactions in the middle part of the protein are disrupted- shows the secondary structures.
  3. Intermediate state B- the rest of the segments are disrupted- bonds between beta sheets and beta sheets and alpha helices are disrupted
  4. Denatured state- hydrogen bonds holding the secondary structures together break until the linear polypeptide is formed (primary structure)
128
Q

How does the stability of the protein change as it passes through different energy states?

A

During the folding or unfolding process, proteins follow a partly-defined pathway consisting of intermediate states (we can have much more than just 2 intermediate states). That means that the protein must pass through certain energy states. Goes from very thermodynamically stable native state to less stable states with even more energy

129
Q

How does an individual protein’s folding pathway change over time?

A

If the denatured state protein reforms the native state and the protein begins to go through the denaturing pathway again, the new intermediate proteins in each state will not exactly resemble the proteins in the corresponding states from the first time around. It will follow a pathway that is similar in energy, however.

130
Q

Amyloidoses

A

Diseases that result from the formation of protein aggregates, called amyloid fibrils or plaques. Alzheimer disease is an example of this. An abnormally folded aggregate serves as a nucleus to recruit more proteins.

131
Q

How do acetyl groups impact protein function?

A

Many proteins are acetylated at the terminal amine group to prevent degradation by our cells

132
Q

Lack of appropriate protein modification can cause

A

Pathological conditions. Examples- lack of vitamin C prevents hydroxylation of protein in collagen, which leads to scurvy. Lack of vitamin K prevents carboxylation of clotting proteins, which can lead to hemorrhaging.

133
Q

Green fluorescent protein (GFP)

A

Comes from a jellyfish. Can be attached to cellular proteins using molecular biology techniques. GFP fluoresces green when exposed to blue light, allowing the cellular location of the attached protein to be determined and even followed

134
Q

Vitamin C/ascorbic acid function

A

Antioxidant, facilitates iron absorption by reducing it to an Fe +2 state. It necessary for both hydroxylation of proline and lysine in collagen synthesis and dopamine beta-hydroxylation, which converts dopamine to NE.

135
Q

Vitamin C deficiency

A

Scurvy- symptoms include swollen gums, hemarthrosis (bleeding into joint cavity), anemia, poor wound healing, weakened immune response.

136
Q

Hydroxyl groups

A

Collagen, the most abundant protein in our body, contains proline amino acids that contain hydroxyl groups. These hydroxyl groups stabilize the structure. Collagen gives tissue strength and has a quaternary structure. In a disease called scurvy, a deficiency in vitamin C leads to the inability to produce hydroxyproline in collagen. This leads to a decrease in tissue strength. Vitamin C is necessary for proline modification

137
Q

Carboxyl groups

A

In a protein called prothrombin, the glutamate amino acids contain carboxyl groups. Without these groups, prothrombin cannot work properly and this can lead to hemorrhage. Prothrombin is used to stop bleeding

138
Q

Sugar groups

A

Many proteins that are destined for the cell membrane or secretion are modified with sugar groups. These make them more hydrophilic or polar, which increases their ability to interact with other proteins or other hydrophilic molecules

139
Q

Phosphoryl groups

A

Epinephrine, a hormone and neurotransmitter, can act on serine and threonine amino acids by phosphorylating them. These can act as triggers to turn on or off many types of cellular processes. This is how insulin is turned on or off

140
Q

Cleavage of polypeptides

A

Many proteins in the body are produced in their inactive form. To activate these proteins, special enzymes cleave peptide bonds in the active proteins, making them active. Examples are: digestive enzymes (chymotrypsin), blood clotting protein (fibrin), and hormones (adrenocorticotropic hormone- ACTH)

Biochemistry (13 decks)

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