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Biochem midterm 2 > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

What R groups can be associated with the polar phosphate group of a glycerophospholipid?

A 
Ethanolamine
Choline
Serine 
Glycerol
myo-inositol 4,5-bisphosphate
phosphatidyl-glycerol
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2
Q

What type of link is implicated between the fatty acid and the glycerol in a glycerophospholipid and a triglycerol?

A

Ester bond/link

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3
Q

What R groups can be associated to form the head of a sphingolipid and what different molecule can they form?

A

Phosphocholine: sphingomyelin
Glucose: cerebroside
Di, tri or tetrasaccharide
Complex oligosaccharide: ganglioside

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4
Q

What is the bond implicated in the linkage of sphingosine and fatty acid and what does this bond form?

A

amide link/bond

form Ceramide

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5
Q

What type of bond is implicated in the linkage of a polar head group and sphingosine?

A

phosphodiester linkage

or glycosidic linkage

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6
Q

What is the blood type of an individual with no active glycosyltransferase?

A

O

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7
Q

What is the blood type of an individual with a glycosyltransferase that transfers an N-acetylgalactosamine group?

A

A

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8
Q

What is the blood type of an individual with a glycosyltransferase that transfers galactose?

A

B

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9
Q

What is the difference between a sterol and a steroid?

A

steroid does not possess the alkyl chain, making them more polar than sterols

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10
Q

Which eicosanoids will be implicated in inflammation and fever and in the contraction of the smooth muscle of the uterus during labor?

A

Prostaglandins

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11
Q

Which eicosanoids will be implicated in the formation of blood clots by vasoconstriction and facilitate platelet aggregation?

A

thromboxanes

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12
Q

Which eicosanoids will be implicated in smooth muscle contraction in the lungs?

A

leukotrienes

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13
Q

What is an aldose?

A

carbonyl group connected to an H and a R group

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14
Q

What is a ketose?

A

Carbonyl group connected to 2 R groups

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15
Q

What is an isomer?

A

Compounds with the same empirical formula but different connectivity

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16
Q

What is a stereoisomer?

A

Compounds with the same empirical formula and same connectivity but with different arrangement in 2D or 3D

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17
Q

What group defines the configuration L or D of a carbohydrate?

A

The hydroxyl group

which is the most distant to the carbonyl group in a molecule with many chiral centers

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18
Q

What is an enantiomer?

A

Compounds that are mirror images, but that are not surimposable. All the OH groups around the different chiral centers are inversed.

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19
Q

What is a diastereomer?

A

Stereoisomer that are not mirror images.

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20
Q

What is an epimer?

A

Diastereomers that differ only at one chiral center.

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21
Q

What is the name of the standard five-carbon sugar?

A

Ribose

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22
Q

What is the name of the standard 6 carbon sugar?

A

Glucose

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23
Q

What is the result of the attack by alcohol on aldehydes?

A

Hemiacetals

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24
Q

What is the result of the attack by alcohol on ketones?

A

Hemiketals

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25
Q

What is an alpha anomer?

A

the hydroxyl group is on the opposite side of the ring as the CH2OH moiety (in a cyclic monosaccharides)

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26
Q

What is a beta anomer?

A

the hydroxyl group is on the same side of the ring as the CH2OH moiety (in a cyclic monosaccharide)

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27
Q

What do we call the conversion between an alpha and a beta anomer?

A

mutarotation

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28
Q

What are called the six members oxygen-containing rings?

A

Pyranoses

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29
Q

What are called the five members oxygen-containing rings?

A

furanoses.

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30
Q

What is the general composition of a nucleotide?

A

nitrogenous base
pentose
phosphate

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31
Q

What is the general composition of a nucleoside?

A

nitrogenous base

pentose

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32
Q

What is the difference between ribose and deoxyribose?

A

Ribose possesses a hydroxyl group at the 2nd carbon and deoxyribose possessed a H groups at the same position

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33
Q

Which nitrogenous bases are purines and what distinguishess them from pyrimidines?

A

Adenine and guanine

2 rings, 9 atoms total. with 2 N per rings

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34
Q

Which nitrogenous bases are pyrimidines and what distinguishes them from purines?

A

Cytosine
Thymine (DNA)
Uracil (RNA)
1 ring, 2N

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35
Q

What kind of bond connects the pentose ring and the nitrogenous base? (tell at what position is the bond in purines and pyrimidines)

A

N-glycosidic bond on the N1 position in pyrimidine and

N9 position in purine

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36
Q

What bond links the 3’ carbon atom of the sugar molecule and the 5’ carbon atom of another?

A

Phosphodiester bonds.

Phosphate on the 5’ carbon and hydroxyl on the 3’ carbon

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37
Q

What is implied in the Chargaff rule?

A

The amount of guanine equals to cytosine and the amount of adenine equals to thymine which means that
A+G=C+T
(purines= pyrimidines)

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38
Q

What is the difference between RNA and DNA in alkaline conditions?

A

RNA is more unstable in alkaline conditions because the 2’ hydroxyl acts as a nucleophile in an intramolecular displacement. (break down of RNA)
DNA which lacks 2’ hydroxyls is more stable.

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39
Q

What conditions can induce DNA denaturation?

A

high temperature or change in pH.

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40
Q

What does the loss of base stacking in DNA denaturation do?

A

Increase UV absorbance.

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41
Q

What factors will increase the midpoint of melting in DNA?

A

High GC content
Long DNA
High salt content

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42
Q

What is deamination?

A

Spontaneous mutagenesis –> loss of the exocyclic amino group.

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43
Q

What is depurination?

A

purine is loss by hydrolysis of the N-B-glycosyl bond

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44
Q

What conditions will induce dimerization of pyrimidines?

A

UV light exposition.

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45
Q

Name the main mutagenesis implied in DNA molecules?

A

deamination
depurination
Dimerization of pyrimidine
Ionizing radiation (causes ring opening and strand breaking)

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46
Q

What are the other functions of nucleotides that are not DNA compounds?

A 
Energy source (NTP hydrolysis)
Coenzymes (CoA)
Regulatory molecule (second messenger (cAMP))
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47
Q

What are the three fundamental rules of replication?

A
  1. replication is semiconservative
  2. Replication begins at an origin and proceeds bidirectionally
  3. Synthesis of a new DNA occurs in the 5’–>3’ direction and is semi discontinuous.
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48
Q

What confirmed the hypothesis of a semiconservative model for DNA replication?

A

The presence of intermediate hydrid band of N14-N15 in the Meselson-Stahl experiment.

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49
Q

Which experiment showed that DNA replication is bidirectional?

A

Cairn’s experiment

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50
Q

Which experiment showed that the replication always begins at the same location?

A

Inman’s experiment.

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51
Q

What is the correction mechanism contained in almost all DNA polymerases?

A

3’–>5’ exonuclease activity. “proofreading”

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52
Q

What correction mechanism is proper to DNA pol 1?

A

5’–> 3’ exonuclease activity. (remove the primer)

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53
Q

What is the function of helicase?

A

use ATP to unwind DNA strands

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54
Q

What is the function of topoisomerase?

A

relieve the stress caused by unwinding

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55
Q

What is the function of DNA-binding protein?

A

stabilize separated strand. keep the DNA opened.

56
Q

What is the function of primase?/

A

make RNA (more rarely DNA) primers

57
Q

What is the function of DNA ligase?

A

seal nick between successive nucleotides on the same strand (Okazaki fragments)

58
Q

DNAa binds to what sites?

A

R and I sites on the origin of replication

59
Q

What is the role of the DUE (tandem) sequence in oriC?

A

high A-T composition so easy denaturation by DNAa forces binding to oriC sites.

60
Q

What are the main DNA proteins that acts in the initiation of replication?

A

DNAa, DNAb(helicase), DNAc (helps the process)

61
Q

Is the replication speed rate the same for leading and lagging strands?

A

no, slower on the lagging side, little bit behind the leading strand elongation.

62
Q

How is the RNA primer removed?

A

Removed by DNA pol 1 or RNaseH1.

63
Q

Which energy source does the DNA ligase need in order to seal the nick?

A

AMP

64
Q

What are the protein and sequence needed for the replication fork to stop?

A

protein TUS

sequence TER

65
Q

What is the role of DNA topoisomerase IV in the termination of replication?

A

separated the catenated chromosomes.

66
Q

What are the two common properties of lipids?

A
  1. insolubility in aqueous or water-based solution

2. Solubility in organic or non-polar solvents

67
Q

What is a fatty acid?

A

Amphipathic molecules with carboxylic group bind to hydrocarbon chains containing between 3 to 35 carbons

68
Q

What is a saturated fatty acid?

A

no double bonds in the hydrocarbon chain

69
Q

What is an unsaturated fatty acid?

A

Presence of double bonds on the hydrocarbon chain

70
Q

Where do we start to count the carbons in the delta nomenclature?

A

Start at the COOH group.

71
Q

When do we start to count the carbons in the omega nomenclature?

A

Starts at the CH3 group.

72
Q

How does the solubility of fatty acids change?

A

Decreases as the chain length increase

longer= less soluble

73
Q

How does the melting point of fatty acids change?

A

decreases as the chain length decreases
shorter=lower melting point
decreases as the number of double bonds increases
more unsaturated= lower melting point

74
Q

Which fatty acids have a lower melting point?

A

unsaturated cis fatty acids

cis=kink=disordered= more easily disrupted.

75
Q

How can trans fatty acids be artificially formed?

A

partial hydrogenation

76
Q

What are the basic components of a triglyceride?

A

3 fatty acids

glycerol

77
Q

What type of linkage bonds the glycerol and the fatty acids in a triglyceride?

A

ester linkage

78
Q

What are the advantages of fat instead of complex sugar for energy storage?

A

Fatty acids contains more energy (more reduced)

Carry less water (non polar)

79
Q

What is the process for crude soap production?

A

(Hydrolysis with strong acids or base) Add a strong base to a triacylglycerol –> formation of a glycerol and a fatty-COO-H+ which is the crude soap.

80
Q

How do we separate the fatty acids and the glycerol for energy production?

A

hydrolysis with lipases

81
Q

What is the chemical composition of waxes

A

esters of long-chain saturated and unsaturated fatty acids with long-chain alcohols.

82
Q

What is the basic composition of a phospholipid?

A

2 fatty acids
Phosphate group+ head group
L-Glycerol-3-Phosphate.

83
Q

What is the major component of most eukaryotic cell membranes?

A

Phosphatidylcholine

84
Q

What determines the type and net charge of a glycerophospholipid?

A

the head-group

85
Q

Where are located the fatty acids on the glycerol backbone of phospholipids?

A

on the C1 (fatty acid saturated) and C2 (fatty acid unsaturated) carbons

86
Q

Where is located the phosphate group of the glycerol backbone of phospholipids?

A

C3

87
Q

What is the backbone of the sphingolipid?

A

sphingosine

88
Q

What molecules are degrading phospholipids?

A

Phospholipases A1, A2, C, D

89
Q

What is the basic composition of a sterol?

A

four fused rings (3–> 6 carbons, 1 –> 5 carbon)
Hydroxyl group forming polar head
Various non-polar side chains

90
Q

What enzyme is used in the Colorimetric Glucose Analysis?

A

Glucose oxidase

91
Q

What bond links two sugar molecules between an anomeric carbon and hydroxyl carbon?

A

Glycosidic bond

92
Q

What is a nonreducing disaccharides?

A

Two sugars linked by an glycosidic bond between two anomeric carbon

93
Q

What is an amino sugar?

A

An OH group of a sugar is replaced by an NH2 group by amidation process.

94
Q

What is a deoxy sugar?

A

An OH group is replaced with an H group in a sugar.

95
Q

What is an acidic sugar?

A

Sugar that contain a carboxyl group.
O=C-O-
Confers a negative charge at neutral pH.

96
Q

Starch is a mixture of two compounds. What are they?

A

Amylose –> unbranched polymer of alpha 1 –>4 residues
Amylopectin: polymer of alpha 1–>4 residues but with a branch point alpha 1–>6 linkers occurring every 24-30 residues part

97
Q

Where does the stacking of sugar occurs in a polysaccharide?

A

reducing ends.

98
Q

What is glycogen?

A

glucose monomers form alpha 1–>4 linked chain, with branched points with alpha 1–> 6 linkers every 8-12 glucose residues.

99
Q

What enzyme degrades both starch and glycogen at the nonreducing ends?

A

alpha-amylase

100
Q

What is cellulose?

A

Water insoluble polymer of unbranched homopolysaccharide of glucose.

101
Q

Where do we find cellulose?

A

Cell wall of plants.

102
Q

What is the function of glycogen?

A

main storage polysaccharide in animals

103
Q

What is the function of starch?

A

main storage polysaccharide in plants

104
Q

What is the most abundant polysaccharide in nature?

A

Cellulose

105
Q

What enzyme degrade cellulose?

A

Cellulase.

present in bacteria, fungi and protozoa.

106
Q

What are the functions of carbohydrates in addition to proteins?

A

cell-cell interaction
stabilizes proteins against degradation. (surface proteins)
Role in the proper folding of proteins.

107
Q

What consensus sequence is implied in a N-linked oligosaccharides and where does it connect on a protein?

A

Asn-AA-Ser
Asn-AA-Thr
link to the amide nitrogen of an Asn amino acid.

108
Q

The N-linked oligosaccharides are added to what type of proteins?

A

destined to the extracellular side of the cell membrane

109
Q

The O-linked oligosaccharide are added to what type of proteins?

A

destined to intracellular or extracellular side of the cell membrane

110
Q

What consensus sequence is implied in O-linked oligosaccharides and where does it connect on a protein?

A

No known consensus sequence.

Connected to the hydroxyl group of a Ser of Thr amino acid.

111
Q

What is a glycoconjugate?

A

Carbohydrates covalently linked to other non-carbohydrate biomolecules.

112
Q

What are the functions of glycoconjugates?

A

Cell to cell recognition and signalling
Labelling of proteins
Hold cell together in the extracellular matrix

113
Q

What are proteoglycans?

A

Rod-shaped protein in a cell membrane that are covalently linked to carbohydrates. (specifically GAGs)

114
Q

What is the sequence of the core protein that links the glycosaminoglycans?

A

Ser-Gly-X-Gly

115
Q

What are syndecans?

A

protein that has a single transmembrane domain anchoring it to a membrane ( integral membrane protein)

116
Q

What are glypicans?

A

Protein that is covalently linked to a lipid in the membrane

117
Q

What is a glycosaminoglycan?

A

Linear polymers of repeating disaccharide units

118
Q

What are the particularities of hyaluronate?

A

GlcA - GlcNAc
No sulfate groups
Found in articular cartilage and synovial fluid

119
Q

What are the particularities of Chondroitin

A

GlcA - GalNAc4S

Found in cartilage around joints

120
Q

What are the particularities of Keratan sulphate?

A

Gal- GlcNac6S
No sugar-acid uronic acid
found in cornea, cartilage and bone.

121
Q

What are the particularities of heparin?

A

IdoA2S- GlcNS3S6S
Sometime GlcA
Anticoagulant

122
Q

What are the functions of heparan sulfate?

A

Prevent blood clotting by activating inhibitor antithrombin
Binding to various cells regulates the development and formation of blood vessels
Can also bind to viruses and bacteria and decrease their virulence.

123
Q

What are the main components of the extracellular matrix?

A

proteoglycan aggregates
collagen fibers
elastin

124
Q

What are the three components of the structure of lipopolysaccharide?

A

Lipid A region
Core region
O-specific chain region

125
Q

What compounds are more likely to form micelles?

A

free fatty acids
detergent
some steroids
phospholipids with only one fatty acid

126
Q

What compounds are more likely to form a bilayer?

A

Phospholipids

Sphingolipids

127
Q

What forces are stabilizing the membranes?

A

hydrophobic effect
Van der Waals
electrostatic interaction

128
Q

What is impermeable to a membrane?

A

charges ion and large molecules or proteins

129
Q

What is permeable to a membrane

A

hydrophobic molecules and neutral gases and water.

130
Q

What are the two monosaccharide units usually contained in the disaccharides of glycosaminoglycans

A

N-acetyl-glucosamine
N-acetyl-galactosamine
and
uronic acid

131
Q

What compounds are linked by an N-glycosidic bond?

A

Nitrogenous base+ pentose

132
Q

What compounds are linked by an ester bond?

A

Glycerol + fatty acids

Glycerol phosphate + fatty acids

133
Q

What compounds are linked by a phosphodiester bond?

A

2 nucleotides
sphingosine+ head group
phosphatidic acid+ head group

134
Q

What compounds are linked by an amide bond?

A

sphingosine + fatty acid

135
Q

What compounds are linked by an O-glycosidic bond?

A

2 sugar rings.

136
Q

What compounds are linked by a tetrasaccharides bridge?

A

glycosaminoglycans + protein

Biochem midterm 2 (3 decks)

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