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122.101 Biochemistry of Cells > Exam and Test Study > Flashcards

Exam and Test Study Flashcards

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1
Q

What side chain does the amino acid Phe have?

A

A Ch2 connected to a aromatic ring.

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2
Q

What side chain does the amino acid Lys have?

A

(Ch2)4 connected to an NH3+.

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3
Q

What side chain does the amino acid Ala have

A

A Ch3.

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4
Q

What side chain does the amino acid Gly have?

A

An H.

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5
Q

What side chain does the amino acid Ser have?

A

An -OH.

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6
Q

What side chain does the amino acid Cys have?

A

A Ch2 connected to an SH.

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7
Q

Why do we need energy and enzymes to build a macromolecule?

A

Because more order is added to the system with every monomer added. Increasing order and decreasing entropy requires energy.

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8
Q

How does the cell get the energy to the reaction?

A
  • By adding the energy first via activated monomers.

- By coupled reactions (where one reaction releases energy and the other reaction uses it).

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9
Q

What are the need to know facts about peptide bonds?

A
  • Planar
  • Partial double bond character
  • Almost always trans
  • Capable of hydrogen bonding
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10
Q

What is a protein domain?

A

A discrete section of a single polypeptide.

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11
Q

What is tertiary structure?

A

Irregular folding of a protein formed mostly be weak interactions between side chains.

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12
Q

What is protein conformation maintained by?

A

Weak interactions between amino acid side chains.

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13
Q

What is a salt bridge?

A

Positively-charged amino group of lysine side chain can form an ionic interaction with the negatively-charged carboxyl end of aspartate side chain.

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14
Q

What is the hydrophobic effect?

A

Achieving the lowest energy state in aqueous solution. This dynamic state is entropically unfavourable.

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15
Q

What are covalent disulphide bonds?

A

Bonds that from between -SH groups of cysteine side chains that are close together in the tertiary structure.

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16
Q

What is protein quaternary structure?

A

The arrangement of two or more discrete polypeptide subunits into a single, functional oligomeric protein complex.

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17
Q

What is the function of a-keratin?

A

Found in epithelial cells (lines cavities in the body and covers flat surfaces). Hard keratin is found in skin, wool, hair, nails, hooves, claws and feathers etc.

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18
Q

What is the primary structure of a-keratin?

A

Rich in hydrophobic amino acids.
Higher than normal number of cys residues for disulphide bonding.
Typically arranged into an imperfect heptad.

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19
Q

What is the secondary structure of a-keratin?

A

The central region of each polypeptide chain forms a right-handed helix. Two helical strands wrap together into a superhelical coiled coil. There is a parallel arrangement of the two strands. The supercoil is twisted in a left-handed manner. When the two helices touch, there are hydrophobic amino acid residues; their side chain R-groups interlock.

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20
Q

What is the function of collagen?

A

Collagen is found in dense and loose connective tissues.

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21
Q

What is the function of dense connective tissues?

A
  • Tendons and ligaments

- Bones, teeth and cartilage

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22
Q

What is the function of loose connective tissues?

A

Allows body to respond to movements.

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23
Q

What are the properties of connective tissues?

A

These tissues are flexible, elastic under pressure and return to original position. Collagen fibres in these structures provide strength.

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24
Q

How is the structure of collagen related to its function in dense connective tissue?

A

Parallel fibrils of collagen are arranged into bundles or sheets connected to bone or cartilage. It is inelastic due to additive internal strength of many molecules.

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25
Q

How is the structure of collagen related to its function in loose connective tissue?

A

Fibrils of collagen are arranged into network perpendicular to the stress. The net formation can reshape without the fibres it is made of being stretched and it can readily return to it’s original shape afterwards.

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26
Q

What is the primary structure of collagen?

A

Little variety in amino acids. Every third residue is glycine. Contains modified amino acids. Mostly repeating Gly-X-Pro or Gly-X-Hyp units.

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27
Q

What is the collagen superhelix structure?

A

Three polypeptide strands that are wound together in a right-handed superhelical coiled-coil structure.

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28
Q

What are globular proteins?

A
  • Compact and spherical molecules
  • Mostly water soluble
  • Hydrophobic core with hydrophillic exterior
  • Well defined tertiary structure
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29
Q

What is haemoglobin?

A

Oxygen delivery protein in red blood cells.

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30
Q

What is myoglobin?

A

Oxygen storing protein in muscle tissue.

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31
Q

What do red blood cells do?

A
  • Deliver O2 to the body tissues via the blood flow in the circulatory system.
  • Take O2 from the lungs or gills, and release it while squeezing through the body’s capillaries.
32
Q

What is the quaternary structure of haemoglobin?

A
  • Tetramer
  • Contains two identical a-units and two identical B-units
  • Each subunit has one heme molecule which can bind O2.
33
Q

What is heme?

A

Heme is non-protein component that binds O2. Heme has a substituted porphyrin structure.

34
Q

What role does heme play in carbon monoxide poisoning?

A

Heme binds reversibly to carbon monoxide and too oxygen. CO can block binding of O2 to heme because free heme binds CO 25,000 times more strongly than O2. CO binding reduces O2 concentration in blood - which in turn causes carbon monoxide poisoning.

35
Q

Why is CO binding less favourable when Heme is in myoglobin or haemoglobin?

A

Because His E7 prevents co-binding in its preferred (linear) orientation.

36
Q

What graph curve does Mb produce with oxygen binding?

A

Hyperbolic.

37
Q

What graph curve does Hb produce with oxygen binding?

A

Sigmodial.

38
Q

What is different about the structure of Hb that gives it a different O2 binding curve?

A

Hb is a tetramer and each of the subunits has an associated heme molecule. The subunits are not identical; there are two a-globin and two B-globin subunits in each tetrameric Hb molecule.

39
Q

What is unusual about the primary structure of keratin?

A

There are a lot of hydrophobic amino acids (Ala, Val, Leu etc). Usually every 4th amino acids is hydrophobic and there is a heptad repeat.

40
Q

What is unusual about the primary structure of collagen?

A

Every third amino acid is glycine. There are many proline and hydroxyproline residues. Lots of Gly-X-Pro and Gly-X-Hyp sequences.

41
Q

At the single polypeptide level, how do the helical structures formed by keratin and collagen differ?

A

a-keratin - typical right-handed a-helix with H-bonds along the axis of the helix and side chains extending outwards.

Collagen - left-handed helix, H-bponding not possible within helix. More elongated and smaller diameter helix than a-helix.

42
Q

How many polypeptides are included in the coiled coil of keratin?

A

2

43
Q

How many polypeptides are included in the coiled coil of collagen?

A

3 (tropocollagen)

44
Q

What direction does the keratin coiled-coil wind?

A

Left-handed

45
Q

What direction does the collagen coiled-coil wind?

A

Right-handed

46
Q

What bonds/interactions keep the keratin coiled coil together?

A

Hydrophobic interactions and interlocking of hydrophobic side chains.

47
Q

What bonds/interactions keep the collagen coiled coil together?

A

Hydrogen bonds between helices of the superhelix. Between polar C=O and -NH groups of peptide bonds in the centre of the helix.

48
Q

What is the main advantage of the coiled coil structure?

A

There is more than one strand and they are coiled in two directions, the structure does not stretch.

49
Q

What bonds link the coiled coil structures into fibrils and fibres in keratin?

A

Disulphide bonds.

50
Q

What bonds link the coiled coil structures into fibrils and fibres in collagen?

A

Lysine cross-bridges.

51
Q

What is unusual about the collagen helix?

A

It is more tightly wound and more elongated than an a-helix.

52
Q

What unusual amino acids are found in the collagen primary structure, and what is their role?

A

Hydroxyproline and hydroxylysine. Repair of collagen.

53
Q

Why is vitamin C important in our diet?

A

It is needed to form hydroxyproline and hydroxylysine in collagen. Without it, collagen doesn’t form correctly and it cannot be repaired.

54
Q

What are the important features of the tertiary structure of myoglobin?

A
  • monomeric protein
  • globular protein
  • hydrophobic centre and surface
  • hydrophobic pocket containing heme group
55
Q

What is the name of the non-protein component of Mb?

A

Haem.

56
Q

Which metal ion is bound to harm?

A

Fe2+

57
Q

How many molecules of oxygen can bind to an Mb molecule?

A

One.

58
Q

How well does CO bind to free Haem compared to oxygen?

A

25,000 X better than O2

59
Q

How well does CO bind to myoglobin compared to oxygen?

A

200 X better than O2.

60
Q

What is the side chain of proline?

A

A pentose with an NH in it.

61
Q

What is the side chain of aspartate?

A

A Ch2 connected to a carboxylic acid

62
Q

What are the three essential amino acid residues in chymotrypsin?

A

Serine 195
Histidine 57
Aspartate 102

63
Q

What part of the active site of chymotrypsin determines its specificity?

A

The hydrophobic pocket - hydrophobic side chain fits here.

64
Q

What essential residue can be considered ‘least essential’ in chymotrypsin?

A

Aspartate 102. It holds histidine in the correct tautomeric form so it can interact with serine. If it is not there then then enzyme is 10,000 times slower.

65
Q

Explain why an enzyme might be stereospecific?

A

The substrate has to fit into the active site for a reaction to occur. An optical simmer of the same molecule is unlikely to fit correctly.

66
Q

What is a catalyst?

A

Something that increases the rate of a reaction but is unchanged at the end of the reaction.

67
Q

What are the two main types of secondary structure found in proteins?

A

A-helices and B-pleated sheets.

68
Q

What is a globular protein?

A
  • Compact
  • Spherical molecule
  • Mostly water soluble
  • Hydrophobic core and hydrophillic exterior
69
Q

What is the structure of an intracellular soluble globular protein?

A

Primary structure: Polypeptide or chain of amino acids
Secondary structure: a-helices or B-pleated sheets
Tertiary structure: polar/hydrophobic amino acids on outside and nonpolar/hydrophilic amino acids on the inside.

70
Q

How does allosteric control of an enzyme operate?

A

Allosteric enzymes bind to the enzyme at a different place than the active site by weak interactions. When an effector binds, a conformational change results, affecting the binding of substrate at the active site.

71
Q

What is Km?

A

A measure of affinity of the enzyme for its substrate.

72
Q

What is the essential active site residues?

A

If the enzyme is altered by protein engineering or chemical modification to remove any essential resides, then the activity will be lost.

73
Q

How does an enzyme bind a specific substrate?

A

Enzymes position substrates in the correct conformation and orientation for the active site. All or part of the substrate enters the active site and binds to the enzyme.

74
Q

What are the similarities between Hb and Mb>

A
  • Both have iron protein as central metal
  • Both globular proteins
  • Both have ligand as O2
    Both have similar overall structures
75
Q

List the overall important facts about Hb.

A
  • Tetrameric protein
  • Oxygen delivery in RBC’s
  • 4 subunits; 2 alpha and 2 beta
  • Has a heme group noncovalently bonded
  • Different arrangements of amino acids in different animals
  • Sigmodial curve
76
Q

List the overall important facts about Mb.

A
  • Monomeric protein
  • O2 storage in muscles
  • Hyperbolic curve
  • Single polypeptide chains
  • Has a heme molecule also
77
Q

What is chymotrypsin?

A

A protease in the small intestine.

122.101 Biochemistry of Cells (3 decks)

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