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DBCS Biochem > Amino Acids and Proteins (Collagen) > Flashcards

Amino Acids and Proteins (Collagen) Flashcards

1
Q

Biomolecules contain many different types of ____ and ______ groups

A

Polar and non-polar

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2
Q

What are the different parts of the structure of an amino acid in this picture?

A
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3
Q

What are the nonpolar side chains? (6)

A
  1. Glycine
  2. Alanine
  3. Valine
  4. Leucine
  5. Isoleucine
  6. Methionine
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4
Q

Of the nonpolar sidechains, these are the hydrophobic sidechains (4)

A
  1. Valine
  2. Leucine
  3. Isoleucine
  4. Methionine
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5
Q
  1. This AA is a nonpolar aliphatic sidechain with a unique cyclic structure, it is more conformationally restricted that other sidechains. It’s not as common due to it’s unusual properties.
  2. It is important for what structure?
A
  1. Proline
  2. Collagen helix
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6
Q

These are the AAs with aromatic side chains. Aromatic means it has a phenyl group. They are mostly nonpolar but some can form hydrogen bonds

A
  1. Phenylalanine (Phe, F)
  2. Tyrosine (Tyr, Y)
  3. Tryptophan (Trp, W)
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7
Q

This aromatic AA is important due to its OH group which makes it more reactive

A

Tyrosine

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8
Q

What is unique about the phenyl structure of aromatic side chains?

A

Delocalized electrons

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9
Q

These are the hydrophilic AA side chains

A
  1. Serine (Ser, S)
  2. Threonine (Thr, T)
  3. Asparagine (Asn, N)
  4. Glutamine (Gln, Q)
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10
Q
  1. What parts of the hydrophilic sidechains make them polar?
  2. What types of bonds are they able to form, as donors or receptors?
A
  1. Hydroxyl or amine groups
  2. Hydrogen Bonds
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11
Q

This is a less polar but more reactive analog of serine

A

Cysteine

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12
Q
  1. What group of cysteine makes it very reactive?
  2. What types of bonds does that group often form?
A
  1. -SH (thiol group), it is more reactive than -OH
  2. Disulfide bridges
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13
Q

These are the AAs with charged hydrophilic side chains

A
  1. Lysine (Lys, K)
  2. Arginine (Arg, R)
  3. Histidine (His, H
  4. Aspartate (Asp, D)
  5. Glutamate (Glu, E)
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14
Q

These are the negatively charged, acidic AAs at a pH of 7.4

A
  1. Aspartate
  2. Glutamate
  3. Histidine (kinda)
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15
Q

These are the positively charged, basic AAs

A
  1. Lysine
  2. Arginine
  3. Tyrosine (kinda)
  4. Cysteine (kinda)
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16
Q

These are linear chains of covalently linked AAs. They have a regular main chain and variable side chains.

A

Proteins (polypeptides)

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17
Q
  1. Does synthesis of proteins require energy?
  2. Are the peptide bonds stable?
A
  1. Yes! (ribosomes translate from mRNA)
  2. Yes
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18
Q
  1. Polypeptide chains are directional, meaning the go from the ___–>____ end
  2. For a protein with N amino acids, how many different polypeptide chains are possible?
A
  1. N–>C end (amino to carbonyl end) Note that AA #1 has a free Amino group, the last AA has a free Carboxyl group
  2. 20N (permutation)
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19
Q

What types of bonds covalently crosslink different segments of a protein chain

A

Disulfide bonds

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20
Q

The structure of a biologially active protein consisting of L-amino acids linked by peptide bonds in a precisely defined sequence. It can have disulfide bonds holding two chains together.

A

Primary Structure

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21
Q

What determines the 3D structure of a protein?

A

The sequence of amino acids

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22
Q

What primary structure did Fred Sanger elucidate in 1953?

A

Bovine Insulin

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23
Q
  1. In the secondary structure of proteins, what bond forces a planar structure?
  2. Why?
A
  1. Peptide Bond
  2. The delocalized electrons on nitrogen give it double bond like characteristics (it’s flat)
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24
Q
  1. In the secondary structure of proteins, what configuration is favored among AAs to avoid steric clashes, cis or trans?
  2. Which AA is the exception?
A
  1. Trans
  2. Proline, (note that both configurations, cis and trans, can produce steric clashes for Pro)
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25
Q
  1. How many atoms are there in the main chain of a peptide bond?
  2. Which atom in the chain allows for flexibility and rotation, leading to proteins adopting different structures?
A
  1. Six
  2. Cα (alpha carbon)
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26
Q
  1. Which bonds are fixed in the secondary structure of proteins?
  2. Which bonds can rotate?
A
  1. CO-NH bonds (peptide) are fixed
  2. Cα-CO and Cα-NH
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27
Q
  1. This right handed secondary protein structure turns counter clockwise
A

Alpha helix

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28
Q

How many AAs away is another AA when they hydrogen bond in an Alpha Helix?

A

4

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29
Q

On the same side of an alpha helix, what interact with one another?

A

Side chains (2,3,6), may be important for function

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30
Q

This is the favored secondary structure for secondary protein structure

A

ß-Strand

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31
Q

Is the separation between amino acids greater in the alpha helix or ß-strand?

A

Greater in the beta strand by more than 2x what the alpha helix is (3.5Å vs 1.5Å)

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32
Q

What does the beta strand form which is even more common?

A

Beta sheet

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33
Q

Parallel or anti-parallel ß-sheet?

A

Antiparallel

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34
Q

Parallel or anti parallel ß-sheet?

A

Parallel (pay attention to N–>C direction)

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35
Q

In this protein secondary structure, side-chains alternate upward and downward from the plane of the sheet

A

ß-Sheet

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36
Q

Strands of the ß-sheet adopt a LEFT/RIGHT handed twist

A

Right

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37
Q

In the tightly packed tertiary structure of proteins, folding is driven by the burial of ________ residues from water. It is driven by charge, entropy, hydrogen bonding.

A

Hydrophobic. When water is condensed around a protein, the hydrophobic aspects will fold and bury away from the condensed water.

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38
Q

Which AAs (protein residues) are largely found on the interior of the tertiary structure of proteins?

A

Nonpolar (Val, Leu, Ile, Met, and Phe

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39
Q

Which AAs (protein residues) are largely found on the surface of the tertiary structure of proteins?

A

Charged residues (Arg, His, Lys, Asp, Glu)

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40
Q

Which AAs are usually on the surface of the tertiary structure of proteins but frequently found on th einterior as well

A

Polar uncharged (Ser, Thr, Asn, Gln, Tyr and Trp)

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41
Q

Where do hydrogen bonds form between donors and acceptors on the tertiary structure of proteins?

A

Interior,hydrogen bonds are buried.

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42
Q

This is an example of a tertiary protein structure in the body

A

Myoglobin

43
Q
  1. What part of myoglobin binds oxygen?
  2. What atom is within it?
A
  1. The heme group
  2. Iron
44
Q

What secondary protein structure comprises myoglobin?

A

Alpha helices

45
Q

These are 30-400 amino acid units of a large protein that fold independently into discrete globular units and that are connected by shorter peptide linker regions. They may interact with one another

A

Domains

46
Q

This protein structure is the symmetrical organization of identical subunits (protomers) of multi-chain proteins

A

Quarternary structure

47
Q

What type of quaternary symmetry is this?

A

Twofold quaternary symmetry

48
Q

These are 4 elements of the tertiary structure of proteins. What are they?

A
  1. Disulfide Bonds
  2. Hydrogen Bonding
  3. Salt Bridges
  4. Hydrophobic interactions
49
Q

Collagen has a specialized protein structure called the…

A

Triple helix

50
Q

The collagen monomers in the triple helix are LEFT/RIGHT handed

A

Left handed

51
Q

The triple helix of collagen is LEFT/RIGHT handed

A

Right handed

52
Q

What category of protein structure is the collagen triple helix?

A

Quaternary (symmetrical identical units)

53
Q

Are the individual collagen chains alpha helices?

A

No! Alpha chains.

54
Q

Collagens are ______, composed of three helical peptide chains designated to α

A

Heterotrimers

55
Q

A type I collagen heterotrimer is composed of what? (other collagens have different chain combinations)

A

Two α1 chains and one α2 chain

56
Q
  1. Every third residue is what AA in collagen chains?
  2. What other AAs occur frequently (2)
A
  1. Gly
  2. Pro/Hyp
57
Q

What function does Hyp serve in the collagen helix?

A

Makes it more stable by allowing hydrogen bonding

58
Q

How do the individual collagen chains (alpha chains) in the collagen triple helix differ from the alpha helix? (3)

A
  1. Left handed coiling
  2. Chains are more extended (3.0Å rise/residue and 3.3 residues/turn)
  3. No hydrogen bonds within individual chains
59
Q

Why doesn’t an individual collagen strand have hydrogen bonding within it?

A

Pro/Hyp don’t have H donors to interact with

60
Q

How is the triple helix of collagen stabilized?

A

H-bonds between the individual strands

61
Q
A
62
Q

Tight supercoiling of collagen helical chains is possible because small _____ sidechains point to interior and large ____/_____ sidechains point to exterior

A

Gly chains point to interior, Pro/Hyp point to exterior (allowing H bonding)

63
Q
  1. This member of the collagen family is a fibril associated collagen with interrupted triple helices
  2. This type of collagen is important for hydroxyapatite crystals
  3. This type forms mesh/networks that are important for basement membranes and hemidesmosomes
A
  1. FACIT
  2. Type I
  3. Type IV
64
Q

This type of collagen is present in bone, tendon, dentin, and skin as banded fibers with a transverse periodicity of 64 nm. It provides tensile strength

A

Type I

65
Q

This type of collagen is observed in hyaline and elastic cartilage as fibers that are thinner than type I

A

Type II collagen

66
Q

This type of collagen is present in the basement membrane as a component of reticular fibers.

A

Type III collagen

67
Q
  1. This is the first collagen type that is synthesized by wound healing
  2. It is eventually replaced by what other type?
A
  1. Type III
  2. Type I
68
Q
  1. This type of collagen is associated with the basal lamina. One single molecule of it will bind to the laminin binding site
  2. Does it form bundles?
A
  1. Type IV collagen
  2. No, just single strands
69
Q

This type of collagen is observed in the amnion and chorion of the fetus, and in muscle tendon sheaths.

A

Type V collagen

70
Q
  1. What are the fibrillar collagens which provide tensile strength to tendons, ligaments, and skin?
  2. Their chains associate in a staggered manner via ______ interactions and covalent crosslinks between ____ and ______
A
  1. Type I, II, III, V, XI
  2. Hydrophobic, His & Lys
71
Q

In the formation of fibrillar collagen, a _______ array of collagen molecules results in a fibril. The regular overlap of the short, non-helical termini of the collagen chains results in a banded pattern.

A

(electron density makes ends appear darker)

72
Q

This is the term for sugars attaching to proteins

A

Glycosylation

73
Q
  1. Where does the biosynthesis a of collagen occur in the cell?
  2. Where does the post-translational processing occur?
  3. It is then secreted into this place where it is trimmed of extension peptides and assmebled into fibrils
A
  1. Rough Endoplasmic Reticulum
  2. Golgi Apparatus
  3. Extracellular Space
74
Q

This molecular chaperone helps collagen chains assemble by helping them orient so they can spontaneously assemble the triple helix

A

HSP 47

75
Q
  1. This is collagen that hasn’t had the end pieces removed yet
  2. This is collagen that has had the end pieces removed but hasn’t yet been crosslinked to another helix
  3. To become mature collagen, what residue has to cross link?
A
  1. Procollagen (yellow in the picture)
  2. Tropocollagen
  3. Lys
76
Q
  1. An inmportant first step in the formation of collagen is the hydroxylation of ____ and _____ residues
  2. What does the hydroxylation provide?
A
  1. Pro and Lys
  2. Stablization of collagen through interchain H bonding
77
Q
  1. What molecule is important for the hydroxylation of pro and lys in the formation of collagen
  2. What’s its role?
A
  1. Vitamin C (ascorbate)
  2. It maintains the +2 oxidation state of Iron (Fe)
78
Q
  1. During collagen crosslink formation, these are the precursors of the crosslink
  2. What are the two processes through which this can occur?
A
  1. Allysine (and hydroxyallysine)
  2. Aldol Condensation and Schiff base (imine) intermediates
79
Q

Do covalent and non-covalent interactions stabilize the collagen fiber?

A

Yes.

80
Q

A mutation in COL1A1 and COL1A2 genes, which encode the alpha chains of type 1 collagen, interferes with the conversion of procollagen to collagen. It leads to defective crosslinking and reduction in the tensile strength of tendons rich in type I collagen. It’s observed in some form of this…which includes hyperextensible skin and hypermobile joints, and defects can extend to blood vessels or organs resulting in rupture or detachment (retina)

A

Ehlers-Danlos syndrome

81
Q

This condition can also cause scarring that resembles crumpled cigarette paper

A

Ehlers-Danlos Syndrome

82
Q

This is a collagen disorder that causes thin dentin and varies in severity. Blue sclera, altered teeth, hearing loss (hypoacusis), long bone and spine deformities, and joint hyperextensibility

A

Osteogenesis Imperfecta

83
Q

There are 3 other proteins in the extracellular matrix of collagen, they are…

A
  1. Elastin (main protein of elastic fibers)
  2. Fibronectin
  3. Laminin
84
Q

What is this a picture of? 4 lysines can be adjacent to one another to form it

A

Elastic structure (check with Patston)

85
Q
  1. This is the major component of the basal lamina
  2. It consists of three polypeptide chains, α ß γ, linked by….(variants of each chain give rise to several isoforms of the protein)
A
  1. Laminin
  2. Disulfide bonds
86
Q
  1. Laminins have binding sites for cell surface surface receptors like these…
  2. Also for this type of collagen
  3. And this other protein
A
  1. Integrins
  2. Type IV (present in basal lamina)
  3. Nidogen, aka enactin
87
Q

Laminin monomers self-associate to form a network that is part of the…

A

Basal Lamina

88
Q

This is a glycoprotein formed by two identical chains joined by disulfide linkages close to the C-terminal

A

Fibronectin

89
Q

This type of fibronectin is secreted by hepatocytes and is secreted into the blood stream

A

Plasma Fibronectin

90
Q

This type of fibronectin is produced by fibroblasts and forms part of the extracellular matrix

A

Cellular Fibronectin

91
Q

Fibronectin has binding sites for 4 things..

A
  1. Integrins
  2. Collagen
  3. Heparan Sulfate
  4. Fibrin
92
Q
  1. These are negatively charged polymers of repeating disaccharide units containing an amine sugar
  2. They are very POSITIVELY/NEGATIVELY charged
  3. The charge allows them to bind to…
  4. They have a lot of this molecule…
A
  1. Glycosaminoglycans
  2. Negatively
  3. Water
  4. Sulfate (SO3-)
93
Q

GAGs often form gels, so where are they found?

A

Joints but also other tissues

94
Q

Lack of ability to degrade GAGs can lead to…

A

Skeletal deformities and short life expectancy

95
Q
A
96
Q

These are proteins with attached GAGs

A

Proteoglycans

97
Q

That vast majority of proteoglycans are…

A

GAGs (95%)

98
Q

These function as joint lubricants, structural components in connective tissue, mediators of the cell adhesion matrix, and in storage of growth factors

A

Proteoglycans

99
Q

Proteoglycan aggregates are form by:

  1. An axial _____ molecule
  2. Core proteins attached to the above molecule by____ proteins
  3. _________s which are attached to the core protein
    4.
A
  1. Hyaluronan molecule
  2. Linker proteins
  3. GAGs
100
Q

Several chains of GAGs bound to a core protein forms a…

A

Proteoglycan (look at picture)

101
Q

Associations between proteoglycans and hyaluronic acid form ____ in the extracellular matrix. The extension of this structure yields a 3D array of proteoglycans bound to HA, which creates a stiff matrix or ‘bottlebrush’ structure in which collagen and other ECM components are embedded

A

Aggrecan

102
Q

This is a molecule that is present in the plasma membrane of many epithelial cells. What type of molecule is it?

A

Proteoglycan. Note that more than one GAG can be present and that N or O linked oligosaccharides may be present

103
Q

A defect in lysosomal enzymes which degrades GAGs leads to the accumulation of GAGs and proteoglycans in cells, leading to a variety of diseases called

A

mucopolysaccharidoses

DBCS Biochem (3 decks)

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