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Biology > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

If a molecule has n chiral centers, how many possible stereoisomers are there?

A

2^n

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2
Q

What property is different between enantiomers? (Shape doesn’t count)

A

Polarization of light

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3
Q

What is the term for a mixture that contains a 50/50 combination of enantiomers

A

Racemic

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4
Q

What kind of bond is broken in ATP when utilizing it as an energy source?

A

Phosphoanhydride

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5
Q

What term describes two genes of the same origin in the same organism?

A

Paralogs

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6
Q

What term describes two genes of the same origin in different organisms?

A

Orthologs

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7
Q

What term describes two genes of the same origin? (Produced from duplication)

A

Homologs

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8
Q

What term describes the structure taken by amphipathic molecules when they aggregate and form a hydrophilic interface

A

Micelles

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9
Q

The pH of a buffer solution is determined by what equation?

A

Henderson-Hassalbalch

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10
Q

What kind of buffer system is employed by our circulatory system for our blood?

A

Bicarbonate Buffer System

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11
Q

What kind of buffer system is employed by our cells for our cytosol?

A

Phosphate Buffer System

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12
Q

What part of an amino acid is its chiral center?

A

Alpha carbon

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13
Q

Assuming the R group is at the bottom and the H group is at the top, what term describes an amino acid with its amine on the left?

A

L-Amino Acid

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14
Q

Assuming the R group is at the bottom and the H group is at the top, what term describes an amino acid with its amine on the right?

A

D-Amino Acid

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15
Q

In what form are most biological enantiomers of amino acids?

A

L Stereoisomer

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16
Q

What term describes the dimeric amino acid formed from two cysteine residues covalently bound at sulfur?

A

Cystine

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17
Q

What term describes the amino acid composed of four lysine reduces found in elastin?

A

Desmosine

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18
Q

What term describes an amino acid that has charges but a net zero charge

A

Zwitterion

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19
Q

What term describes an amino acid that can act as both an acid and base?

A

Ampholyte

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20
Q

The pH at which most ions exist in their zwitterion form is referred to as what?

A

Isoelectric pH (pI)

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21
Q

What constant describes the extent that an acid dissociates in solution

A

Acid dissociation constant

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22
Q

What equation describes how to calculate the acid dissociation constant

A

[CB] * [H+] / [Acid]

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23
Q

What term relates the acid dissociation constant to pH by converting it to a -log of 10?

A

pKa

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24
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + [CB] / [Acid]

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25
Q

When pH = pKa and the pH causes equal amounts of weak acid and its conjugate base, what is this point known as?

A

Half Equivalence Point

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26
Q

In a titration curve, the X axis measures?

A

Volume of Strong Base

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27
Q

In a titration curve, the Y axis measures?

A

pH

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28
Q

Are buffers most effective at
a) Half-Equivalence Points
b) Isoelectric Points
c) Neither

A

a) Half-Equivalence Points

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29
Q

All amino acids have at least how many half-equivalence points and why?

A

Two because they all have at least an amine group and carboxyl group?

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30
Q

How many half equivalence points does glycine have?

A

2

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31
Q

Multi-subunit proteins with at least two identical polypeptides are called what?

A

Oligomers

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32
Q

What term describes the relationship between the two identical polypeptides in an oligomer?

A

Protomers

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33
Q

Conjugated Proteins consist of what two elements?

A

Protein + Prosthetic Group

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34
Q

What method involves slowly separating out unwanted substances from a crude extract through a semipermeable membrane?

A

Dialysis

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35
Q

What compound is utilized for the process of salting out due to its extremely high solubility?

A

Ammonium Sulfate

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36
Q

What kinds of specialized chromatography amplifies small distances by multiplying the speed that substances travel through a column?

A

High-Performance Liquid Chromatography (HPLC)

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37
Q

What chemical process can be utilized to sequence the primary structure of proteins by removing the N-terminus amino acid of the peptide?

A

Edman Degradation

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38
Q

What type of mass spectrometry utilizes a laser (that inhibits fragmentation) [soft ionization]

A

MALDI MS

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39
Q

What type of mass spectrometry applies a high voltage charge to a liquid for soft ionization?

A

ESI MS (Electrospray Ionization)

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40
Q

What type of mass spectrometry breaks down proteins into peptides and then fragments specific peptides into y-type ions or b-type ions which can be compared to analyze amino acid differences and can sequence them?

A

Tandem MS (MS/MS)

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41
Q

In synthesis of peptides, what kind of column anchors the amino acid?

A

Polystyrene

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42
Q

The amine group is protected during peptide synthesis by what chemical compound?

A

FMOC

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43
Q

An amino acid with FMOC is attached to the polypeptide chain using what chemical compound?

A

DCC

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44
Q

What sulfur-based reducing agent is very common in the cell?

A

Glutathione

45
Q

What amino acids make up glutathione?

A

Glutamate, Glycine, Cysteine

46
Q

The phi angle is between what two parts of a peptide?

A

The amine group and alpha carbon

47
Q

The psi angle is between what two parts of a peptide?

A

The carboxyl group and alpha carbon

48
Q

The omega angle is between what two parts of a peptide?

A

The carboxyl group and amine group between two amino acids

49
Q

What kind of plot graphs psi angle against the phi angle?

A

Ramachandran Plot

50
Q

What amino acid can occupy white spaces in a Ramachandran Plot?

A

Glycine

51
Q

What type of secondary structures can be found in the 1nd quadrant of a Ramachandran plot?

A

Left-handed alpha helix

52
Q

What type of secondary structures can be found in the 3nd quadrant of a Ramachandran plot?

A

Right-handed alpha helix

53
Q

What type of secondary structures can be found in the 2nd quadrant of a Ramachandran plot?

A

Antiparallel and Parallel beta sheets, collagen triple helix.

54
Q

What amino acid has the greatest tendency to form alpha helices?

A

Alanine

55
Q

What two amino acids are “helix disruptors” that are not found in alpha helices?

A

Glycine and Proline

56
Q

What kind of charge is typically exhibited towards the C terminus and N terminus respectively?

A

Positive and Negative

57
Q

What kind of beta sheets are longer?

A

Antiparallel

58
Q

What kind of beta sheets are more stable structurally?

A

Antiparallel

59
Q

What amino acid is typically found in its cis form in beta turns?

A

Proline

60
Q

How many amino acid residues do Type 1 and Type 2 beta turns have? What about gamma turns?

A

4 and 3

61
Q

Chiral molecules do not have mirrored properties, and so what kind of method can measure the difference in properties between enantiomers to determine structure composition?

A

Structural Dichroism

62
Q

In N-acetylglucosamine, instead of a ___ group there is a ____

A

Hydroxyl; Amine group bound to acetate

63
Q

What kind of carbohydrate acid is formed from oxidizing the aldehyde group

A

Aldonic acid

64
Q

What kind of carbohydrate acid is formed from oxidizing the hydroxyl group of the terminal carbon

A

Uronic acid

65
Q

What kind of carbohydrate acid is formed from oxidizing both the hydroxyl group of the terminal carbon and aldehyde

A

Aldaric acid

66
Q

Some monosaccharides can be oxidized by mild oxidizing agents such as?

A

Cu2+ (cupric ion)

67
Q

When the anomeric carbon of a saccharide forms a glycosidic linkage with oxygen of another compound, what kind of glycosidic linkage is it?

A

O-glycosyl bond

68
Q

When the anomeric carbon is joined to a nitrogen in a protein or nitrogenous base, what kind of linkage is formed?

A

N-glycosyl bond

69
Q

In a polysaccharide, the end that has a free anomeric carbon is described by what term?

A

Reducing End

70
Q

What kind of macromolecular storage molecule found in bacteria and yeasts is composed of 1’6 alpha linkages and 1’3, 1’4, and sometimes 1’2 alpha linkages for branches?

A

Dextrans

71
Q

In Chitin, subunits of N-acetylglucosamine are connected in what kind of arrangement and resemble what other kind of polysaccharide?

A

1’4 Beta Linkage, Cellulose

72
Q

What are the two conformations of a polysaccharide in solution?

A

Boat and Chair

73
Q

What is the most stable conformation for a polysaccharide in solution

A

Chair Conformation

74
Q

Lysozyme hydrolyzes ____ linkages between ____ and ____ breaking down the ____ molecule.

A

Beta 1’4; N-acetylglucosamine and N-acetylmuramic acid; Peptidoglycan

75
Q

What polysaccharide is found in red algae and contains a mixture of D-galactose, L-galactose, sulfate, and pyruvate?

A

Agar

76
Q

The six-membered ring found in carbohydrates is described by what term?

A

Pyranose ring

77
Q

The five-membered ring found in carbohydrates is described by what term?

A

Furanose ring

78
Q

Glycosaminoglycans are found in what kinds of organisms?

A

Animals and Bacteria

79
Q

What is the term for long strands of carbohydrates found in connective tissue that contain amino groups?

A

Glycosaminoglycans

80
Q

Glycosaminoglycans have either N-acetylglucosamine or N-acetylgalactosamine and what other type of compound?

A

Uronic Acid

81
Q

Glycosaminoglycans can be attached to proteins to form what kind of molecule?

A

Proteoglycans

82
Q

What kind of glycosaminoglycan can be found in vitreous humor and the ECM of tendons? It is also targeted by some pathogenic bacteria.

A

Hyaluronan

83
Q

What kind of glycosaminoglycan is common in sharks and contributes to tensile strtength?

A

Chondroitin Sulfate (Cartilage

84
Q

What kind of glycosaminoglycan lacks uronic acid, has variable sulfur content, and is common in dead cells such as nails?

A

Keratan Sulfates

85
Q

What kind of glycosaminoglycan is responsible for interacting many proteins such as one involved in blood clotting?

A

Heparan Sulfate

86
Q

What is the term for oligosaccharides covalently joined to a protein through N-linkages?

A

Glycoproteins

87
Q

What is the term for proteins that recognize the specialized informational sequences of oligosaccharides?

A

Lectins

88
Q

A plasma membrane component whose hydrophilic headgroup is an oligosaccharide and is rich in the brain is described by what term?

A

Glycosphingolipid

89
Q

What amino acid residues are used to link proteoglycans to oligosaccharides in O-linkages?

A

Threonine or Serine

90
Q

What amino acid residues are used to link proteoglycans to oligosaccharides in O-linkages?

A

Asparagine

91
Q

What heparan-sulfate proteoglycans have a single transmembrane domain, three extracellular domains, and regulate cell communication?

A

Syndecans

92
Q

What heparan-sulfate proteoglycans are attached to the membrane by a lipid anchor that is derived from phosphatidylinositol?

A

Glypicans

93
Q

What glycans with large numbers of O-linked oligosaccharides are present in mucus secretions?

A

Mucins

94
Q

What glycosphingolipids have an oligosaccharide called sialic acid?

A

Gangliosides

95
Q

Gangliosides are strongly located in what kind of tissue, in what portion of the membrane, and with what kind of charge?

A

Nervous, Outer Leaflet, Negative.

96
Q

Luteinizing Hormone and Thyrotropin have N-linked oligosaccharides, why is this special?

A

They are recognized by lectins on hepatocytes which causes a cyclic concentration in plasma

97
Q

What plasma protein carries most blood copper and aids in iron metabolism?

A

Ceruloplasmin

98
Q

What special sialic acid residue protects ceruloplasmin and erythrocytes from degradation?

A

N-acetylneuraminate or Neu5ac

99
Q

What plasma membrane lectins mediate cell-cell recognition and adhesion?

A

Selectins

100
Q

What kind of selectins on endothelial cells and leukocytes respectively are involved in margination?

A

P and E-selectins; L-selectins.

101
Q

What sialidase is utilized by influenza?

A

Neuraminidase

102
Q

What type of restriction endonuclease is primarily utilized for genetic engineering?

A

Type II

103
Q

What is the primary benefit to restriction endonucleases that provide sticky ends over blunt ends?

A

They facilitate covalent linkage of DNA ligase

104
Q

What are four/five necessary inclusions within a plasmid that is specifically utilized as a cloning vector?

A

Ori sequence, relatively small size, linkers / polylinker, selectable markers, screenable markers.

105
Q

During transformation, plasmid DNA is incubated with E.coli, what are two things utilized to enhance the likelihood of transformation?

A

Heat Shock and a Calcium Chloride solution.

106
Q

What kind of method utilizes a high voltage electrical pulse to induce temporary permeability into the membrane for large molecules such as plasmids to travel through?

A

Electroporation

107
Q

After creating your plasmid that confers resistance to Tetracycline, you attempt transformation with a batch of E. coli cells, you then transfer your batch of E. coli to a petri dish containing Tetracycline to determine what bacteria successfully received the plasmid, what term describes this process?

A

Positive Selection

108
Q

After creating your plasmid that contains a gene that codes for an enzyme that breaks down protein X, you attempt transformation with a batch of E. coli cells, you then transfer your batch of E. coli to a petri dish containing substance Y, which interacts with protein X and promotes cell death. You do this to determine what bacteria successfully received the plasmid, what term describes this process?

A

Negative Selection

109
Q
A

Biology (6 decks)

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