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Biochemistry 2 > Chapter 2- Proteins > Flashcards

Chapter 2- Proteins Flashcards

1
Q

Proteins are made of

A

Amino acids

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2
Q

Protein complexes

A

Proteins interact with each other and with other macromolecules to form more complicated assemblies. Protein in complexes can act synergistically to generate capabilities that individual proteins might lack. Examples include the macromolecular machines that replicate DNA, transmit signals in cells, and allow muscle cells to contract

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3
Q

Sarcomeres

A

Muscle cells contain multiple myofibrils that are each made of numerous repeats of a complex protein assembly (called a sarcomere). The interdigitation of filaments, made up of many individual proteins, causes the banding pattern of a sarcomere

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4
Q

Actin and myosin

A

Myofilaments that help the muscle to contract

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5
Q

Vitamin D and muscle contraction

A

Important for normal skeletal muscle development and in optimizing muscle strength and performance

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6
Q

Calcium and muscle contraction

A

Calcium triggers contraction by reacting with regulatory proteins and allowing the function of actin and myosin. In the absence of calcium, the regulatory proteins prevent the interaction of actin and myosin

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7
Q

Lactoferrin

A

On binding iron, the protein lactoferrin undergoes a substantial change in conformation that allows other molecules to distinguish between the iron free and iron bound forms

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8
Q

How many amino acids are there?

A

20

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9
Q

Protein isomers

A

When 4 different groups are bonded to the a-carbon, the amino acids are chiral, which means that they exist as two mirror image forms called the L isomer and the D isomer. Only L isomers are found in proteins. L and D isomers are mirror images of each other

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10
Q

5’ end of proteins

A

Contains the amine (NH2) group, considered upstream

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11
Q

3’ end of proteins

A

Contains the carboxyl (COO-) group, also referred to as the poly A end

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12
Q

Protein configuration

A

The configuration around the carbon atom is called S if the progression from the highest to the lowest priority is counterclockwise. The configuration is called R if the progression is clockwise. Most amino acids have the S configuration

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13
Q

How is the priority of the different substituents of a carbon atom determined?

A

The 4 different substituents of an asymmetric carbon atom are assigned a priority according to atomic number. The lowest priority substituent, often hydrogen, is pointed away from the viewer

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14
Q

Amino acid side chains vary in terms of (6)

A

size, shape, charge, hydrogen bonding capacity, hydrophobic character, and chemical reactivity

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15
Q

4 classes of amino acids

A

hydrophobic, polar, positively charged, and negatively charged

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16
Q

Charge

A

Charge refers to likely charge at physiological pH

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17
Q

Hydrophobic amino acids (9)

A
  1. Glycine (Gly, G)
  2. Alanine (Ala, A)
  3. Proline (Pro, P)
  4. Valine (Val, V)
  5. Leucine (Leu, L)
  6. Isoleucine (Ile, I)
  7. Phenylalanine (Phe, F)
  8. Methionine (Met, M)
  9. Tryptophan (Trp, W)
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18
Q

Phenylketonuria (PKU)

A

A disease caused by an autosomal recessive mutation. Your body can’t break down phenylalanine, which builds up in the blood and causes problems with cognition and other issues

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19
Q

Hydrophobic amino acids properties

A

The hydrophobic amino acids have side chains that lack the ability to interact well with polar substances like water

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20
Q

Tryptophan

A

The bulkiest hydrophobic amino acid. It contains an indole group in its side chain. The indole group is joined to a methylene (-CH2-) group. The indole is composed of two fused rings containing an NH group. Tryptophan is a little less hydrophobic due to its side chain NH group

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21
Q

Maple syrup urine disease

A

An autosomal recessive inherited disorder. People are unable to break down leucine, isoleucine, and valine

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22
Q

Polar amino acids (6)

A
  1. Serine (Ser, S)
  2. Cysteine (Cys, C)
  3. Asparagine (Asn, N)
  4. Glutamine (Gln, Q)
  5. Tyrosine (Tyr, Y)
  6. Threonine (Thr, T)
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23
Q

Positively charged amino acids (3)

A
  1. Lysine (Lys-K)
  2. Arginine (Arg-R)
  3. Histidine (His-H)
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24
Q

Arginine

A

Has a long chain that is capped with a guanidinium group (-NH-C-N2H4). The guanidium group is positively charged, making arginine a positively charged amino acid

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25
Q

Histidine

A

Contains an imidazole group (a pentagon with 3 carbons and 2 nitrogens), which is an aromatic ring that can be positively charged. Histidine is considered a positively charged amino acid. The imidazole group has a pKa near 6, so it can be uncharged or positively charged near neutral pH, depending on its environment. It can be located at the active sites of enzymes, where the ring can bind and release protons during enzymatic reactions

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26
Q

Negatively charged amino acids (2)

A
  1. Aspartic acid (Asp, D)
  2. Glutamic acid (Glu, E)
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27
Q

Normal pH of the body

A

7.35

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28
Q

How many amino acids have readily ionizable side chains?

A

7- tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acid. These amino acids are able to donate or accept protons to facilitate reactions, as well as to form ionic bonds

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29
Q

Functions of proteins (7)

A
  1. Catalysts
  2. Transport and storage of other molecules (like oxygen)
  3. Mechanical support
  4. Immune protection
  5. Generate movement
  6. Transmission of nerve impulses
  7. Control of growth and differentiation
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30
Q

Primary structure

A

The amino acid sequence of a protein

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31
Q

Secondary structure

A

The 3D structure that is formed when hydrogen bonds develop between amino acids near one another

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32
Q

Tertiary structure

A

Formed by long range interactions between amino acids. It is the overall course of the polypeptide chain of a protein. Protein function depends directly on this 3D structure

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33
Q

Quaternary structure

A

A functional protein made of several distinct polypeptide chains. It refers to the spatial arrangement of subunits and the nature of their interactions. A dimer is the most simple example. Hemoglobin is a more complex example because it forms a tetramer

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34
Q

Enzymes

A

Proteins that catalyze specific chemical reactions in biological systems. The reactive properties of their functional groups are essential to the function of enzymes

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35
Q

Protein functional groups

A

Proteins have a wide range of functional groups- includes alcohols, thiols, thioethers, carboxylic acids, carboxamides, and others. Most of these groups are chemically reactive and account for the broad spectrum of protein function when combined in different sequencies

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36
Q

Which main properties of proteins allow them to have a wide range of functions? (4)

A
  1. The ability of proteins to form 3D structures
  2. The wide variety of protein functional groups
  3. The ability of proteins to interact with other macromolecules to form complexes
  4. Some proteins are rigid, others are very flexible
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37
Q

Rigid proteins

A

Function as structural elements in the cytoskeleton (internal scaffolding), or in connective tissue

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38
Q

Flexible proteins

A

Act as hinges, springs, or levers. The conformational changes in proteins allow for the regulated assembly of large protein complexes and for the transmission of information within and between cells. The conformational change that occurs when lactoferrin binds iron is one example

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39
Q

Amino acid structure

A

An alpha amino acid contains a central carbon atom (an alpha carbon), which is bound to an amino group (NH2), a carboxylic acid (COOH), a hydrogen atom, and a distinct R group

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40
Q

Side chain

A

The amino acid’s distinct R group connected to the central carbon

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41
Q

Dipolar ions

A

Amino acids in solution at neutral pH exist as dipolar ions. The amino acid group is protonated (positively charged) and the carboxyl group is deprotonated (negatively charged). The protonated amino group loses a proton around pH 9.5

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42
Q

Glycine

A

The simplest amino acid, has a single hydrogen atom as its side chain. It is achiral since two hydrogens are bound to the central carbon. It is hydrophobic

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43
Q

Alanine

A

The next simplest amino acid. It has a methyl group (CH3) as its side chain. It is hydrophobic

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44
Q

Methionine

A

Has an aliphatic (more hydrophobic) side chain. The side chain contains a thioether (R-S-R) group. Hydrophobic

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45
Q

Isoleucine

A

A hydrophobic amino acid with a larger hydrocarbon side chain. The side chain of isoleucine contains an additional chiral center

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46
Q

Why are aliphatic side chains especially hydrophobic?

A

These side chains tend to cluster together rather than contact water. This results in the hydrophobic effect. The different sizes and shapes of hydrocarbon side chains allow them to pack together and form tightly packed structures without a lot of empty space

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47
Q

Hydrophobic effect

A

The tendency of hydrophobic groups to come together in the presence of water. It stabilizes the 3D structures of water soluble proteins

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48
Q

Proline

A

Has an aliphatic side chain and is hydrophobic. However, it is unique because the side chain is bonded to both the nitrogen and alpha carbon atoms- this creates a pyrrolidine ring. Proline’s cyclic structure makes it more conformationally restricted than other amino acids

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49
Q

Phenylalanine

A

A hydrophobic amino acid that contains a phenyl ring (a derivative of benzene- it’s missing a hydrogen atom). The ring is attached in place of one of the hydrogen atoms of alanine

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50
Q

Serine

A

Like a version of alanine with a hydroxyl (OH) group attached. It is a polar amino acid

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51
Q

Threonine

A

Resembles valine with a hydroxyl group in place of one of valine’s methyl groups. Polar amino acid. Contains an additional asymmetric center, but only one isomer is present in proteins

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52
Q

Tyrosine

A

A version of phenylalanine with the hydroxyl group replacing a hydrogen atom on the aromatic ring. Polar amino acid

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53
Q

Function of hydroxyl group in amino acids

A

It makes the amino acids more hydrophilic and reactive than hydrophobic amino acids with a similar structure

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54
Q

Asparagine

A

A polar amino acid with a terminal carboxamide (CONH2)

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55
Q

Glutamine

A

A polar amino acid with a terminal carboxamide. Its side chain is one methylene group longer than that of asparagine

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56
Q

Cysteine

A

Structurally similar to serine but contains a sulfhydryl thiol (-SH) in place of the hydroxyl (-OH). A sulfhydryl group is more reactive and can be used to form disulfide bonds, which can stabilize proteins. Polar amino acid

57
Q

Amino acids with complete positive charges are

A

Highly hydrophilic

58
Q

Lysine

A

Has a long side chain that terminates with a primary amino group. This group is positively charged at neutral pH, making lysine a positively charged amino acid

59
Q

Aspartic acid

A

A charged derivative of asparagine, because a carboxylic acid replaced carboxamide. It can be called aspartate because at physiological pH, their side chains don’t have the proton that is present in the acid form, so they are negatively charged

60
Q

Glutamic acid

A

A charged derivative of glutamine, because a carboxylic acid replaced carboxamide. It can be called glutamate because at physiological pH, their side chains don’t have the proton that is present in the acid form, so they are negatively charged

61
Q

Which groups in proteins can be ionized?

A

The terminal alpha amino group and the terminal alpha carboxyl group

62
Q

How did these 20 amino acids become the building blocks of proteins?

A

These amino acids are very diverse in terms of structure and chemical structure, so they allow proteins to have many different roles. Many amino acids were probably available from reactions that took place before the origin of life. Also, other possible amino acids could have been too reactive to be present in organisms

63
Q

Peptide bond

A

The alpha carboxyl group of one amino acid is linked to the alpha amino group of another amino acid through hydrolysis. The amino group loses 2 hydrogens and the carboxyl group loses one oxygen. These bonds are kinetically stable because the rate of hydrolysis is very slow

64
Q

Synthesis of peptide bonds

A

Requires an input of free energy. The formation of the bonds is accompanied by the loss of a water molecule

65
Q

Residue

A

Each amino acid unit in a polypeptide

66
Q

Polypeptide chain

A

A series of amino acids joined by peptide bonds. The ends of the chains are different, so a polypeptide chain has directionality. The amino group at one end is considered the beginning of the chain (5’), and the alpha carbonyl group is considered to be the end (3’). It consists of a regularly repeating main chain (backbone) and a variable part that contains the distinctive side chains

67
Q

Polypeptide backbone

A

The regularly repeating part of a polypeptide chain. It is rich in hydrogen bonding potential.

68
Q

Why is the polypeptide backbone able to form hydrogen bonds?

A

Each residue contains a carbonyl group (CO) which can act as a hydrogen bond acceptor. Except for proline, the backbone also contains an NH group that is a hydrogen bond donor. The groups can interact with each other and functional groups from side chains to stabilize structures

69
Q

Proteins

A

Polypeptide chains that contain between 50 and 2000 amino acid residues

70
Q

Oligopeptides/peptides

A

Polypeptide chains made of small numbers of amino acids

71
Q

Average molecular mass for an amino acid

A

110 g mol ^-1. The mass can also be referred to in kilodaltons

72
Q

Dalton

A

Approximately the mass of a hydrogen atom. Protein mass can be referred to in kilodaltons

73
Q

Disulfide bonds

A

Cross links of the linear polypeptide chain. They are formed by the oxidation of a pair of cysteine residues, and sometimes called a cystine. Intracellular proteins typically lack disulfide bonds, but extracellular bonds usually have several. The number of disulfide bond cross links defines the properties of a protein fiber. Hair and wool have fewer cross links, making them more flexible. Horns, claws, and hooves, have more cross links, and are harder

74
Q

Nondisulfide cross links

A

Rarely, these cross links are derived from other side chains present in proteins. Collagen fibers in connective tissue and fibrin blood clots are strengthened this way

75
Q

Frederick Sanger

A

Determined the amino acid sequence of insulin in 1953. It showed that a protein has a precisely defined amino acid sequence that consists only of L amino acids and is linked by peptide bonds

76
Q

The amino acid sequences of proteins are determined by

A

The nucleotide sequences of genes. Genes code for a complementary RNA sequence, which codes for the protein’s amino acid sequence

77
Q

Why is knowing the amino acid sequence important? (4)

A
  1. Knowing the sequence of a protein is necessary to determine its function
  2. Amino acid sequences determine the 3D structures of proteins
  3. Alterations in amino acid sequence can lead to abnormal protein function and disease (sickle cell anemia, cystic fibrosis)
  4. The sequence of a protein reveals a lot about its evolutionary history- matching proteins can indicate a common ancestor
78
Q

Geometry of the peptide bond

A

The peptide bond is planar. When a pair of amino acids is linked, the alpha carbon atom and the CO group of the first amino acid and the NH group and alpha carbon of the second amino acid lie in the same plane. The bond resonates between a single bond and a double bond. Rotation about the bond is prevented and conformation of the peptide backbone is restricted due to the partial double bond character.

79
Q

Charge of the peptide bond

A

The bond is uncharged, which allows the polymers of amino acids to form tightly packed globular structures

80
Q

Trans configuration of the peptide bond

A

The two alpha carbon atoms are on opposite sides of the peptide bond. Almost all peptide bonds are trans. This is because the cis configuration causes steric clashes between groups attached to the alpha carbon atoms

81
Q

Cis configuration of the peptide bond

A

The two alpha carbon atoms are on the same side of the peptide bond. The most common cis peptide bonds are X-Pro linkages. This is because the nitrogen of proline is bonded to two tetrahedral carbon atoms, limiting the steric differences between the trans and cis forms

82
Q

Single bonds within the amino acid

A

The bonds between the amino group and the alpha carbon atom, and between the alpha carbon atom and the carbonyl group are pure single bonds. This means that the two units can rotate around the bond and take on various orientations, and the protein can fold in different ways

83
Q

Torsion angles

A

Specify the rotations around the bonds between the carbon, amino, and carbonyl groups. Forms phi and psi angles, which are between positive and negative 180. Not all angles of rotation are possible, which limits the number of possible structures of the protein

84
Q

Phi angle

A

The angle of rotation around the bond between the nitrogen and alpha carbon atoms

85
Q

Psi angle

A

The angle of rotation around the bond between the alpha carbon and the carbonyl carbon atoms

86
Q

Rotation directions around bonds in a polypeptide

A

A clockwise rotation around either bond corresponds to a positive value, as viewed from the nitrogen atom toward the alpha carbon atom, or from the alpha carbon atom toward the carbonyl group

87
Q

Alpha helix

A

A rod-like secondary structure. A tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array. It is stabilized because the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated 4 residues ahead in the sequence. All main chain CO and NH groups are hydrogen bonded except for the terminal amino acids

88
Q

Spacing of amino acids in an alpha helix

A

There are 3.6 amino acid residues per turn of the helix. Amino acids that are spaced 3 or 4 apart in the primary sequence are spatially close to each other in the alpha helix, while amino acids spaced two apart in the primary sequence are unlikely to be close to each other in the secondary sequence

89
Q

Screw sense of an alpha helix

A

Can be right handed (clockwise) or left handed (counterclockwise). Right handed helices are more energetically favorable because there are less steric clashes between the side chains and the backbone. Therefore, most alpha helices in proteins are right handed

90
Q

Why don’t all proteins form an alpha helix?

A

Not all amino acids can be accommodated. Valine, threonine, and isoleucine have branching at their beta carbon atom, which can destabilize the alpha helix through steric clashes. Serine, aspartate, and asparagine have side chains that contain hydrogen bond donors/acceptors and that are in close proximity to the main chain. This means the side chains compete for NH and CO groups in the main chain. Proline is a helix breaker because it lacks an NH group, and its ring structure prevents it from assuming the psi value

91
Q

Beta sheets

A

Composed of two or more polypeptide chains (beta strands). The beta strands are almost fully extended, instead of being tightly coiled like an alpha helix. The sheet is formed by linking two or more strands lying next to one another hydrogen bonds. The strands can be parallel, antiparallel, or mixed, and the sheets can include 10 or more strands, but typically has 4 or 5. The sheets can be flat or somewhat twisted. Fatty acid binding proteins are built mostly from beta sheets

92
Q

Antiparallel beta sheets

A

Adjacent strands in a beta sheet that run in opposite directions. The NH group and the CO group of each amino acid are hydrogen bonded to the CO group and NH group of another amino acid on the adjacent chain

93
Q

Parallel beta sheets

A

Adjacent strands in a beta sheet that run in the same direction. For each amino acid, the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand. The CO group is hydrogen bonded to the NH group on the amino acid two residues further along the chain

94
Q

Myoglobin

A

The oxygen storage protein in muscle. It is a single polypeptide chain that is made of 153 amino acids. Myoglobin is very compact, globular protein, and most of the main chain is folded into 8 alpha helices, and the rest of the chain mostly turns and loops between helices- this is the tertiary structure of the protein. The capacity of myoglobin to bind oxygen depends on the presence of heme

95
Q

Globular proteins

A

Tightly packed proteins that form a highly compact structure. These proteins have a lack of symmetry and are soluble in water. They perform a wide amount of functions, including regulatory, signaling, and enzymatic activities

96
Q

How is the distribution of amino acids related to a protein’s folding?

A

The interior of a protein generally consists of nonpolar residues. Charged and polar residues are generally found on the outside of the protein. Hydrophobic residues are excluded from water in an aqueous environment

97
Q

The hydrophobic effect

A

A system is more thermodynamically stable when hydrophobic groups are clustered, instead of being extended into aqueous surroundings. This means that the folding of proteins buries their hydrophobic side chains

98
Q

Amphipathic

A

The alpha helix or beta strand has a hydrophobic face that points into the protein interior and a polar face that points into solution. This also helps to pair all the NH and CO groups by hydrogen bonding, because unpaired groups prefer water

99
Q

Proteins that span biological membranes

A

These proteins have a reverse distribution of hydrophobic and hydrophilic amino acids. Porins are proteins found in the outer membranes of bacteria. They are covered on the outside with hydrophobic residues that interact with neighboring alkane chains. The center of the protein contains many charged and polar amino acids that surround a water filled channel in the middle of the protein. Therefore, the protein is sort of inside out relative to other proteins, but it’s the “exception that proves the rule”.

100
Q

Motifs (supersecondary structures)

A

Combinations of secondary structure that are present in many proteins and frequently exhibit similar functions. A helix-turn-helix is an example

101
Q

helix-turn-helix

A

An alpha helix separated from another alpha helix by a turn. This is a supersecondary structure. It is found in many proteins that bind DNA

102
Q

Domains

A

Polypeptide chains that fold into two or more compact regions that can be connected by a flexible segment of polypeptide chain (like pearls on a string). They range in size from 30 to 400 amino acid residues. The extracellular part of CD4 is an example. Proteins can have domains in common even if their overall tertiary structures are different

103
Q

Fibrous proteins

A

Have long, extended structures that have repeated sequences. These proteins include keratin and collagen. They utilize special types of helices that facilitate the formation of long fibers that serve a structural role

104
Q

Alpha keratin

A

Consists of two right handed alpha helices intertwined to form a left handed superhelix, called an alpha helical coiled coil. It is a member of the coiled-coil proteins superfamily and is an essential component of wool, hair, and skin. The helices are stabilized by weak van der Waals forces and ionic interactions. The pattern of side-chain interactions is repeated every seven residues and forms heptad repeats. The bonding pattern of the helices contributes to the properties of the protein

105
Q

Coiled-coil proteins

A

Two or more alpha helices can entwine to form a stable structure. Alpha keratin is an example, as is the intermediate filaments that contribute to the cytoskeleton and the muscle proteins myosin and tropomyosin. In humans, there are 60 members of this family. Members of the family are characterized by a central region of 300 amino acids that contain heptad repeats

106
Q

Heptad repeat

A

Imperfect repeats of a sequence of 7 amino acids found in the coiled-coil proteins

107
Q

Collagen

A

An extracellular protein that is rod shaped. It has 3 helical polypeptide chains and is almost 1000 residues long. Glycine appears at every third residue in the amino acid sequence. and the sequence glycine-proline-hydroxyproline recurs frequently. The helix does not have hydrogen bond, it is stabilized by steric repulsion of the pyrrolidine rings of the proline and hydroxyproline residues when the chain folds into its helical form.

108
Q

Where do hydrogen bonds form in collagen?

A

Three strands wind around one another to form a superhelical cable that is stabilized by hydrogen bonds between strands. The hydrogen bonds form between the peptide NH groups of glycine residues and the CO groups of residues on the other chains. The interior of the cable is very crowded, and glycine is the only residue that can fit into the interior position

109
Q

Where is collagen typically found

A

It is the main fibrous component of skin, bone, tendon, cartilage, and teeth

110
Q

Hydroxyproline

A

A derivative of proline that has a hydroxyl group in place of one of the hydrogen atoms on the pyrrolidine ring

111
Q

Osteogenesis imperfecta

A

A genetic disease that results from a collagen defect. Other amino acids replace the internal glycine residue, which causes delayed and improper folding of collagen. Symptoms include severe bone fragility and blue sclera

112
Q

Subunit

A

Each polypeptide chain in a quaternary structure

113
Q

Dimer

A

The most simple quaternary structure, containing two identical subunits

114
Q

Hemoglobin structure

A

A type of tetramer (quaternary structure). Consists of two alpha subunits and two beta subunits. Subtle changes in the arrangement of subunits within the hemoglobin molecule allow it to carry oxygen from the lungs to tissues with greater efficiency

115
Q

Christian Anfinsen

A

1950s- worked on the ribonuclease enzyme and demonstrated the relationship between the amino acid sequence of a protein and its confirmation. Anfinsen destroyed the 3D structure of ribonuclease using urea/guanidinium chloride to disrupt the protein’s noncovalent bonds and beta mercaptoethanol to disrupt the disulfide bonds in the protein. The ribonuclease was then fully reduced and was a randomly coiled polypeptide chain devoid of enzymatic activity (it was denatured). When urea and mercaptoethanol were removed, the protein slowly regained enzymatic activity- the enzyme spontaneously refolded and became an active catalyst. It had the same properties as the original enzyme, indicating that the information needed to specify the catalytically active structure of ribonuclease is contained in the amino acid sequence

116
Q

What happened to ribonuclease when it was reoxidized in the presence of urea?

A

The enzymatic activity of ribonuclease was very low. This is because the wrong disulfides formed pairs in urea. 104 cysteines paired to form incorrect disulfides, making the ribonuclease “scrambled”. Mercaptoethanol was required and urea must be removed to regain the original form of the protein. This means that native disulfide pairings of ribonuclease contribute to the stabilization of the thermodynamically preferred structure

117
Q

Two conformational states of protein folding

A

Proteins in the presence of a denaturant have a sharp transition from the folded, native form to the unfolded, denatured form as the concentration of the denaturant increases. A similar sharp transition is observed if denaturants are removed from unfolded proteins, so the proteins fold. This suggests that only these two conformational states are present to any significant extent

118
Q

Cooperative transition

A

The sharp transition between conformational states suggests that protein folding and unfolding is an all or none process resulting from a cooperative transition. As part of the folded protein structure is disrupted under unstable conditions, the interactions between it and the remainder of the protein will be lost. This will destabilize the remainder of the structure. Conditions that lead to the disruption of any part of a protein structure will likely unravel the protein completely

119
Q

Components of a partly denatured protein solution

A

In a half unfolded protein solution, half the molecules are fully folded and half are fully unfolded. Although proteins appear to make a rapid transition, there must be intermediates for such a complex molecule

120
Q

Amyloidoses

A

Some neurological diseases- Alzheimer disease, Parkinson disease, Huntington disease, and prion diseases are referred to as amyloidoses. They result in the deposition of protein aggregates (amyloid fibrils/plaques). These diseases are caused by protein misfolding

121
Q

A common features of amyloidoses is

A

The normally soluble PrP proteins are converted into insoluble fibrils rich in beta sheets. The original form contains alpha helices. The incorrect form is marginally more unstable, but it aggregates and pulls more correct forms into the incorrect form

122
Q

PrP

A

A cellular protein that is normally present in the brain- its function is unclear. Infectious prions are aggregated forms of PrP. PrPSC is the version present in infected brains

123
Q

How does the structure of the protein in the aggregated form differ from that of the protein in its normal state in the brain?

A

Normal PrP contains extensive regions of alpha helix and relatively little beta strand. PrPSC’s structure is unclear, but it seems like parts of the protein that has been in alpha helical or turn conformations have been converted into beta strand conformations. The beta strands of planar monomers stack on one another with their side chains tightly interwoven

124
Q

Protein-only model for prion disease transmission

A

Protein aggregates built of abnormal forms of PrPSC act as sites of nucleation to which other PrP molecules attach. Therefore, prion diseases can be transferred from one individual organism to another through the transfer of an aggregated nucleus

125
Q

Alzheimer disease

A

The brains of these patients contain protein aggregates called amyloid plaques that consist primarily of a single polypeptide called A-beta. This polypeptide is derived from a cellular protein called amyloid precursor protein through the action of specific proteases. Polypeptide A-beta is prone to form insoluble aggregates and cause cell death

126
Q

Posttranslational modifications

A

Alterations in the structure of a protein under its synthesis in the cell. These modifications further expand the array of functions proteins are capable of

127
Q

Acetyl groups

A

Acetyl groups are attached to the amino terminals of many proteins. It is a posttranslational modification that makes these proteins more resistant to degradation

128
Q

Hydroxyl groups

A

A posttranslational modification added to proline residues to stabilize fibers of newly synthesized collagen

129
Q

Scurvy

A

A deficiency of vitamin C results in insufficient hydroxylation of collagen, and the abnormal collagen fibers that result are unable to maintain normal tissue strength

130
Q

Vitamin K deficiency

A

Insufficient carboxylation of glutamate in prothrombin (a clotting protein) can lead to hemorrhage

131
Q

How do different posttranslational modifications make amino acids more hydrophobic or hydrophilic?

A

The addition of sugars makes the proteins more hydrophilic and able to participate in interactions with other proteins. The addition of a fatty acid to an alpha amino group or a cysteine sulfhydryl group produces a more hydrophobic protein

132
Q

Green fluorescent protein (GFP)

A

A protein produced by the jellyfish Aequorea Victoria that emits green light when stimulated with blue light. It can be used by researchers as markers in cells. The source of the fluorescence is a group formed by the spontaneous rearrangement and oxidation of the sequence Ser-Tyr-Gly within the center of the protein

133
Q

Vitamin C

A

Also called ascorbic acid. It is an antioxidant that also facilitates iron absorption by reducing it to an Fe2+ state. It is necessary for the hydroxylation of proline and lysine in collagen synthesis. and the dopamine beta-hydroxylation, which converts dopamine to NE. Vitamin C deficiency can cause scurvy

134
Q

Scurvy symptoms

A

Swollen gums, hemarthrosis, anemia, poor wound healing, weakened immune response

135
Q

Xeroderma pigmentosum

A

Inability to repair DNA dimers caused by UV exposure. Causes dry skin, skin cancer, extreme light sensitivity

136
Q

Types of collagen

A

There are 4 types. Type 1 defects cause osteogenesis imperfecta- COL1A1 and COL1A2 proteins have mutations

137
Q

What does ionizable mean?

A

At specific pH values, each side chain can participate in an acid-base reaction in which it can exchange a hydrogen atom with some other biomolecule.

138
Q

The presence of which two groups typically makes an amino acid polar?

A

OH and NH. There are some exceptions

139
Q

What is a hydrogen bond?

A

A weak interaction that form between a hydrogen atom with a partial positive charge and a more electronegative atom like oxygen or nitrogen. In water, hydrogen bonds form between the partially negative oxygen on one molecule and the partially positive hydrogen on another

Biochemistry 2 (12 decks)

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