Chapter 8: Nucleosides Flashcards
1
Q
Nucleotides aid in many ways to allow for what
A
Cellular Metabolism
2
Q
Nucleosides role in the following
1. ATP/GTP
2. cAMP/cGMP
3. NAD/NADP
4. DNA/RNA
A
- Energy currency during metabolic transactions
- Act as essential chemical links in the response to hormones and other extracellular stimuli
- Structural components of an array of enzyme cofactors and metabolic intermediates (NAD/NADP)
- Constituents of nucleic acids
3
Q
rRNA
A
components of the ribosome
4
Q
mRNA
A
Intermates in protein synthesis
5
Q
tRNA
A
adaptor molecules that translate info in mRNA to specific amino acid sequences
binds to amino acids
recognizes mRNA on the other side
6
Q
ncRNAs
A
Wide variety
spliceosomes for example
7
Q
Pentose
A
sugars
8
Q
components of nucleotides
A
nitrogenous base
Pentose
1 + Phodphste
9
Q
Nucleoside
A
Group without a phosphate
10
Q
Purine
A
Adenine / Gaunine
11
Q
Pyrimidine
A
Cytosine, Thymine, and Uracil
12
Q
Two types of Pentose
A
2’-Deoxy-d-ribose DNA
D-ribose = RNA
13
Q
Deoxyribonucleotides
A
structural units of DNA
14
Q
Ribonucleotides
A
Structural units of RNA
15
Q
Phosphodiester Bonds
A
Covalent bond
links nucleotides together
5’ of one nucleotide and 2’ hydroxyl
16
Q
oligonucleotide vs polynucleotide
A
Oligo - short
Poly - long
17
Q
Basic Characteristics of Pyr/Pur
A
Weakly basic, Aromatic, rigid and planar due to partial double bonds
18
Q
Best wavelength for nucleotides UV absoption
A
260nm
19
Q
A
hydrophobic and ph 7
20
Q
Base pairing rules
A
A - T, U
G - C
21
Q
Primary structure of nucleotides
A
covalent structure and nucleotide sequence
22
Q
Secondary structure of nucleotides
A
regular stable structure
23
Q
Tertiary structure of nucleotides
A
complex folding of large chromosomes or complex tRNA or rRNA structures
24
Q
Watson and Crick Model
A
Minor/Major groove
3 hydrogen bonds G-C
2 hydrogen bonds A-T
25
Parallell and antiparallel of DNA
Parallel phosphodiester bonds go the same
antiparallel - phosphodiester bonds run in the opposite way
26
Antiparallel chains
Complementary
H bonding doesn't contribute significantly to DNA structure stability
27
Double helix is stabilized by
Metal cations and base stacking interactions [van der waals]
28
Very Basics of DNA Rep
Step 1: preexisting or parent strand is separated
step 2: parent strands service as a model for the new d
29
Three forms of DNA
B - form
A - form
Z form
30
Palindromes
same thing read either forward or backward
DNA with inverted repeats
31
Mirror repeat
Sequence is inverted than repeated
32
Hairpin
forms when two comp pieces separated by short stretch decide to base pair but a part at the top with no base pairing
33
Cruciforms
Essentially just 2 hairpins
34
Messenger RNA
moves genetic info to ribsomes
35
Monocistronic
1 mRNA = 1 polypeptide
36
Polycistronic
1 mRNA = 2+ different polypep
37
mRNA strands
single stranded always
in its own right handed helical conformation
Two purines are the strongest in mRNA
stabilized by base stacking
antiparallel
38
Structure of two complemtary RNA
A-form right handed double helix
39
Breaks in secondary syrcu
mismatched unmatched bulges loops
40
The most common type of secondary structure
Hairpin
41
Prokaryotic Ribosomes
70s
small subunits 30s
large subunit 50s
42
Eukaryotic Ribosomes
80s
Small subunits: 40s
Large subunit: 60s
43
adenosine 3' ,5' cyclic monophosphate
cAMP
44
When does the Hydrolysis of DNA and RNA occur? What the rate for both DNA/RNA?
under alkaline conditions
RNA is rapidly hydrolyzed due to the presence oh OH
DNA is not rapidly hydrolyzed be it doesn't have OH
45
Tautomer Structures
interconverted forms
Lactam predominates at normal pH
lactam / lactim / double lactim
46
Solubility of Nucleotides
Hydrophobic and insoluble in 7.0pH water
causes stacking interactions [van der waals and dipole dipole
charged and more stable in acid or alkaline not neutral
47
B-form DNA Structure
10.5 base pairs
36A [3.5nm]
Antiparallel
48
Strongest nucleotide pairing
G-C
49
What three things allow for DNA to occur in multiple different forms?
1. deoxyribose can change positions
2. the backbone has rotation ability
3. Free rotation about the C-1-n-GLYCOSL BOND
50
A - form
Right handed double helix with a wider helix
11bp
tilted plane
favored of waterless environments
51
Z-form DNA Structure
Left handed helix. More skinny and long
zigzag appearance in backbone
12bp
52
Hoogsteen pairing
Non watson crick pairing
53
What forms from hoosteen pairing?
Triplex DNA
54
Tetraplex DNA
four dna strands pair
very stable
55
What process does mRNA aid in?
Transciption
56
Examples of monocistronic
most mRNAs
57
Example s of polycistronic
Usually in bacteria and archaea
58
Structure of complimentary RNA Strands
A-form right handed
double helix
antiparallel
59
How does telemarse aid in cancer formation?
Preventing the shortenin of terlomeres
60
Denaturation vs anneal of DNA
Denature - change pH or temperatures change. Disrupts H bonds and base bastacking
Annealing - process by which two strands rejoin after denaturation process once placed back in prefered conditions [two step processs]
61
Hypochromic effect
Low absorption of UV light when double stranded
62
Hyperchromic effect
increase in uv absorpiton when the strands are denatured
63
denaturation temperature [Tm]
temperature at which 1/2 of DNA is present as single strands
temp increases with g-c pairing content
64
What occurs when denatured regions are in DNA/RNA?
bubbles are formed
often in A=T bp
65
RNA vs DNA duplexes
RNA duplexes are more stable to heat denatured than DNA [20 degrees higher]
a hybrid is generally intermediate
66
Why are RNA duplexes more stable than DNA?
The OH group allows for them to form more H bonds DNA doesnt have one so denatures faster
67
Rate of spontaneous alteration is
generally very slow
68
Deamination reactions
spotaneous loss of excocyclic amino groups
69
Demination of c u
70
Depurination
hydrolysis of the N-b-glycosyl bond between the base and pentose
71
What does UV light cause
cyclcobutane pyrimidine dimers
6-4Photoproduct
72
What does ionizing radiation cause
Ring opening
base fragment
break covalent backbone of nucleic acids
73
Deaminating agents in DNA Damage
Nitrous acid precursors
74
Alkylating agents in DNA Damage
75
cannot pair with c
76
What are the ROS? How do they effect us?
Hydrogen peroxide
hydoryl radical
superide radical
Dmaage DNA
77
Whats respoisnble for most oxidative DNA damage
hydroxyl radicals
78
Which pairing is more methlysated
A-C
79
What is used as a methyl donor for all DNA
80
Chemical synthesis of DNA by __ has been highly effective
Phosphonamidite method
81
Polymerase chain reaction [PCR]
Amplifies DNA we want to see
Relies on DNA polymerases
add primers
82
What does PCR do?
Detect and amplify just one DNA molecule in almost all samples
83
Sanger sequencing
dideoxy chain termination sequencing
84
What nucleotide analogs interrupt synthesis?
Dideoxynucleoside triphosphates [ddNTPs]
85
DNA Sequencing techolobies
next-gen and SMRT
86
Sequencing depth
how many times you sqeunce a specific nucletoide in a genome [an average]
87
Contigs
long continuous sequences that are assembled from overlaps
88
Hydrolysis of nucleoside triphosphates provides
Chemical energy, ATP is most common
89
What happens when ATP is coupled to a reaction with positive free energy change?
ATP hydrolysis shifts the equilibrium to favor product formation
90
Yields of ester linakge and anhyride bond
Ester - 14kj/mol
Anhydride - 30kj/mol
91
How does adenosine aid in cofactor activies
It doesnt not particupate directly in the primary function but its removal reduces co factor actieis
92
Nucleotide bidning fold is
A single protein domain that binds adenosine
93
What are second messangers
compounds made inside a cell after a extracellular chemical signals with receptors
94
Examples of second messangers
Cyclic AMP and cAMP
95
ppGpp
producded in bacteria during amino acid starvation
96
ATP and ADP also serve as
signals
97
Purines [pur]
Adenine [A] Guaninen [G]
98
