Midterm 2 Flashcards
(136 cards)
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
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
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
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
5
Q
What type of bond is implicated in the linkage of a polar head group and sphingosine?
A
phosphodiester linkage
or glycosidic linkage
6
Q
What is the blood type of an individual with no active glycosyltransferase?
A
O
7
Q
What is the blood type of an individual with a glycosyltransferase that transfers an N-acetylgalactosamine group?
A
A
8
Q
What is the blood type of an individual with a glycosyltransferase that transfers galactose?
A
B
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
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
11
Q
Which eicosanoids will be implicated in the formation of blood clots by vasoconstriction and facilitate platelet aggregation?
A
thromboxanes
12
Q
Which eicosanoids will be implicated in smooth muscle contraction in the lungs?
A
leukotrienes
13
Q
What is an aldose?
A
carbonyl group connected to an H and a R group
14
Q
What is a ketose?
A
Carbonyl group connected to 2 R groups
15
Q
What is an isomer?
A
Compounds with the same empirical formula but different connectivity
16
Q
What is a stereoisomer?
A
Compounds with the same empirical formula and same connectivity but with different arrangement in 2D or 3D
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
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.
19
Q
What is a diastereomer?
A
Stereoisomer that are not mirror images.
20
Q
What is an epimer?
A
Diastereomers that differ only at one chiral center.
21
Q
What is the name of the standard five-carbon sugar?
A
Ribose
22
Q
What is the name of the standard 6 carbon sugar?
A
Glucose
23
Q
What is the result of the attack by alcohol on aldehydes?
A
Hemiacetals
24
Q
What is the result of the attack by alcohol on ketones?
A
Hemiketals
25
What is an alpha anomer?
the hydroxyl group is on the opposite side of the ring as the CH2OH moiety (in a cyclic monosaccharides)
26
What is a beta anomer?
the hydroxyl group is on the same side of the ring as the CH2OH moiety (in a cyclic monosaccharide)
27
What do we call the conversion between an alpha and a beta anomer?
mutarotation
28
What are called the six members oxygen-containing rings?
Pyranoses
29
What are called the five members oxygen-containing rings?
furanoses.
30
What is the general composition of a nucleotide?
nitrogenous base
pentose
phosphate
31
What is the general composition of a nucleoside?
nitrogenous base
| pentose
32
What is the difference between ribose and deoxyribose?
Ribose possesses a hydroxyl group at the 2nd carbon and deoxyribose possessed a H groups at the same position
33
Which nitrogenous bases are purines and what distinguishess them from pyrimidines?
Adenine and guanine
| 2 rings, 9 atoms total. with 2 N per rings
34
Which nitrogenous bases are pyrimidines and what distinguishes them from purines?
Cytosine
Thymine (DNA)
Uracil (RNA)
1 ring, 2N
35
What kind of bond connects the pentose ring and the nitrogenous base? (tell at what position is the bond in purines and pyrimidines)
N-glycosidic bond on the N1 position in pyrimidine and
| N9 position in purine
36
What bond links the 3' carbon atom of the sugar molecule and the 5' carbon atom of another?
Phosphodiester bonds.
| Phosphate on the 5' carbon and hydroxyl on the 3' carbon
37
What is implied in the Chargaff rule?
The amount of guanine equals to cytosine and the amount of adenine equals to thymine which means that
A+G=C+T
(purines= pyrimidines)
38
What is the difference between RNA and DNA in alkaline conditions?
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.
39
What conditions can induce DNA denaturation?
high temperature or change in pH.
40
What does the loss of base stacking in DNA denaturation do?
Increase UV absorbance.
41
What factors will increase the midpoint of melting in DNA?
High GC content
Long DNA
High salt content
42
What is deamination?
Spontaneous mutagenesis --> loss of the exocyclic amino group.
43
What is depurination?
purine is loss by hydrolysis of the N-B-glycosyl bond
44
What conditions will induce dimerization of pyrimidines?
UV light exposition.
45
Name the main mutagenesis implied in DNA molecules?
deamination
depurination
Dimerization of pyrimidine
Ionizing radiation (causes ring opening and strand breaking)
46
What are the other functions of nucleotides that are not DNA compounds?
```
Energy source (NTP hydrolysis)
Coenzymes (CoA)
Regulatory molecule (second messenger (cAMP))
```
47
What are the three fundamental rules of replication?
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.
48
What confirmed the hypothesis of a semiconservative model for DNA replication?
The presence of intermediate hydrid band of N14-N15 in the Meselson-Stahl experiment.
49
Which experiment showed that DNA replication is bidirectional?
Cairn's experiment
50
Which experiment showed that the replication always begins at the same location?
Inman's experiment.
51
What is the correction mechanism contained in almost all DNA polymerases?
3'-->5' exonuclease activity. "proofreading"
52
What correction mechanism is proper to DNA pol 1?
5'--> 3' exonuclease activity. (remove the primer)
53
What is the function of helicase?
use ATP to unwind DNA strands
54
What is the function of topoisomerase?
relieve the stress caused by unwinding
55
What is the function of DNA-binding protein?
stabilize separated strand. keep the DNA opened.
56
What is the function of primase?/
make RNA (more rarely DNA) primers
57
What is the function of DNA ligase?
seal nick between successive nucleotides on the same strand (Okazaki fragments)
58
DNAa binds to what sites?
R and I sites on the origin of replication
59
What is the role of the DUE (tandem) sequence in oriC?
high A-T composition so easy denaturation by DNAa forces binding to oriC sites.
60
What are the main DNA proteins that acts in the initiation of replication?
DNAa, DNAb(helicase), DNAc (helps the process)
61
Is the replication speed rate the same for leading and lagging strands?
no, slower on the lagging side, little bit behind the leading strand elongation.
62
How is the RNA primer removed?
Removed by DNA pol 1 or RNaseH1.
63
Which energy source does the DNA ligase need in order to seal the nick?
AMP
64
What are the protein and sequence needed for the replication fork to stop?
protein TUS
| sequence TER
65
What is the role of DNA topoisomerase IV in the termination of replication?
separated the catenated chromosomes.
66
What are the two common properties of lipids?
1. insolubility in aqueous or water-based solution
| 2. Solubility in organic or non-polar solvents
67
What is a fatty acid?
Amphipathic molecules with carboxylic group bind to hydrocarbon chains containing between 3 to 35 carbons
68
What is a saturated fatty acid?
no double bonds in the hydrocarbon chain
69
What is an unsaturated fatty acid?
Presence of double bonds on the hydrocarbon chain
70
Where do we start to count the carbons in the delta nomenclature?
Start at the COOH group.
71
When do we start to count the carbons in the omega nomenclature?
Starts at the CH3 group.
72
How does the solubility of fatty acids change?
Decreases as the chain length increase
| longer= less soluble
73
How does the melting point of fatty acids change?
decreases as the chain length decreases
shorter=lower melting point
decreases as the number of double bonds increases
more unsaturated= lower melting point
74
Which fatty acids have a lower melting point?
unsaturated cis fatty acids
| cis=kink=disordered= more easily disrupted.
75
How can trans fatty acids be artificially formed?
partial hydrogenation
76
What are the basic components of a triglyceride?
3 fatty acids
| glycerol
77
What type of linkage bonds the glycerol and the fatty acids in a triglyceride?
ester linkage
78
What are the advantages of fat instead of complex sugar for energy storage?
Fatty acids contains more energy (more reduced)
| Carry less water (non polar)
79
What is the process for crude soap production?
(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
How do we separate the fatty acids and the glycerol for energy production?
hydrolysis with lipases
81
What is the chemical composition of waxes
esters of long-chain saturated and unsaturated fatty acids with long-chain alcohols.
82
What is the basic composition of a phospholipid?
2 fatty acids
Phosphate group+ head group
L-Glycerol-3-Phosphate.
83
What is the major component of most eukaryotic cell membranes?
Phosphatidylcholine
84
What determines the type and net charge of a glycerophospholipid?
the head-group
85
Where are located the fatty acids on the glycerol backbone of phospholipids?
on the C1 (fatty acid saturated) and C2 (fatty acid unsaturated) carbons
86
Where is located the phosphate group of the glycerol backbone of phospholipids?
C3
87
What is the backbone of the sphingolipid?
sphingosine
88
What molecules are degrading phospholipids?
Phospholipases A1, A2, C, D
89
What is the basic composition of a sterol?
four fused rings (3--> 6 carbons, 1 --> 5 carbon)
Hydroxyl group forming polar head
Various non-polar side chains
90
What enzyme is used in the Colorimetric Glucose Analysis?
Glucose oxidase
91
What bond links two sugar molecules between an anomeric carbon and hydroxyl carbon?
Glycosidic bond
92
What is a nonreducing disaccharides?
Two sugars linked by an glycosidic bond between two anomeric carbon
93
What is an amino sugar?
An OH group of a sugar is replaced by an NH2 group by amidation process.
94
What is a deoxy sugar?
An OH group is replaced with an H group in a sugar.
95
What is an acidic sugar?
Sugar that contain a carboxyl group.
O=C-O-
Confers a negative charge at neutral pH.
96
Starch is a mixture of two compounds. What are they?
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
Where does the stacking of sugar occurs in a polysaccharide?
reducing ends.
98
What is glycogen?
glucose monomers form alpha 1-->4 linked chain, with branched points with alpha 1--> 6 linkers every 8-12 glucose residues.
99
What enzyme degrades both starch and glycogen at the nonreducing ends?
alpha-amylase
100
What is cellulose?
Water insoluble polymer of unbranched homopolysaccharide of glucose.
101
Where do we find cellulose?
Cell wall of plants.
102
What is the function of glycogen?
main storage polysaccharide in animals
103
What is the function of starch?
main storage polysaccharide in plants
104
What is the most abundant polysaccharide in nature?
Cellulose
105
What enzyme degrade cellulose?
Cellulase.
| present in bacteria, fungi and protozoa.
106
What are the functions of carbohydrates in addition to proteins?
cell-cell interaction
stabilizes proteins against degradation. (surface proteins)
Role in the proper folding of proteins.
107
What consensus sequence is implied in a N-linked oligosaccharides and where does it connect on a protein?
Asn-AA-Ser
Asn-AA-Thr
link to the amide nitrogen of an Asn amino acid.
108
The N-linked oligosaccharides are added to what type of proteins?
destined to the extracellular side of the cell membrane
109
The O-linked oligosaccharide are added to what type of proteins?
destined to intracellular or extracellular side of the cell membrane
110
What consensus sequence is implied in O-linked oligosaccharides and where does it connect on a protein?
No known consensus sequence.
| Connected to the hydroxyl group of a Ser of Thr amino acid.
111
What is a glycoconjugate?
Carbohydrates covalently linked to other non-carbohydrate biomolecules.
112
What are the functions of glycoconjugates?
Cell to cell recognition and signalling
Labelling of proteins
Hold cell together in the extracellular matrix
113
What are proteoglycans?
Rod-shaped protein in a cell membrane that are covalently linked to carbohydrates. (specifically GAGs)
114
What is the sequence of the core protein that links the glycosaminoglycans?
Ser-Gly-X-Gly
115
What are syndecans?
protein that has a single transmembrane domain anchoring it to a membrane ( integral membrane protein)
116
What are glypicans?
Protein that is covalently linked to a lipid in the membrane
117
What is a glycosaminoglycan?
Linear polymers of repeating disaccharide units
118
What are the particularities of hyaluronate?
GlcA - GlcNAc
No sulfate groups
Found in articular cartilage and synovial fluid
119
What are the particularities of Chondroitin
GlcA - GalNAc4S
| Found in cartilage around joints
120
What are the particularities of Keratan sulphate?
Gal- GlcNac6S
No sugar-acid uronic acid
found in cornea, cartilage and bone.
121
What are the particularities of heparin?
IdoA2S- GlcNS3S6S
Sometime GlcA
Anticoagulant
122
What are the functions of heparan sulfate?
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
What are the main components of the extracellular matrix?
proteoglycan aggregates
collagen fibers
elastin
124
What are the three components of the structure of lipopolysaccharide?
Lipid A region
Core region
O-specific chain region
125
What compounds are more likely to form micelles?
free fatty acids
detergent
some steroids
phospholipids with only one fatty acid
126
What compounds are more likely to form a bilayer?
Phospholipids
| Sphingolipids
127
What forces are stabilizing the membranes?
hydrophobic effect
Van der Waals
electrostatic interaction
128
What is impermeable to a membrane?
charges ion and large molecules or proteins
129
What is permeable to a membrane
hydrophobic molecules and neutral gases and water.
130
What are the two monosaccharide units usually contained in the disaccharides of glycosaminoglycans
N-acetyl-glucosamine
N-acetyl-galactosamine
and
uronic acid
131
What compounds are linked by an N-glycosidic bond?
Nitrogenous base+ pentose
132
What compounds are linked by an ester bond?
Glycerol + fatty acids
| Glycerol phosphate + fatty acids
133
What compounds are linked by a phosphodiester bond?
2 nucleotides
sphingosine+ head group
phosphatidic acid+ head group
134
What compounds are linked by an amide bond?
sphingosine + fatty acid
135
What compounds are linked by an O-glycosidic bond?
2 sugar rings.
136
What compounds are linked by a tetrasaccharides bridge?
glycosaminoglycans + protein
