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92 Cards in this Set

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What is the composition of nucleosides?
base + pentose
What is the composition of nucleotides?
base + pentose + phosphate
What is pentose?
5 member sugar (ribose or deoxyribose)
What is the nucleotide base group?
either purine or pyrimidine
What distinguishes structurally speaking the purines from the pyrimidines?
purine = 2 rings
pyrimidines = 1 ring
Name the purines
Adenine and guanine
Name the pyrimidines?
cytosine, thymine, uracil
Which nucleotide base is in DNA but not RNA?
Which nucleotide is in RNA but not DNA?
4 (abbr.) nucleotides in DNA?
4 (abbr.) nucleotides in RNA?
The 2 pentoses?
ribose (RNA) and deoxy-ribose (DNA)
Both ribose and deoxy-ribose are what kind of rings?
beta furanose rings
Each sugar in DNA has one less what then RNA?
one less -OH group (see slides, very clear) will see H group in RNA where you see an OH group in DNA
The nucleoside of adenine associated with RNA?
The nucleoside of adenine assoc. with DNA?
The nucleoside of guanine assoc. with RNA?
The nucleoside of guanine assoc. with DNA?
The nucleoside of cytosine associated with RNA?
The nucleoside of cytosine associated with DNA?
The nucleoside of thymine associated with DNA?
thymidine or deoxythymidine (thymine is not associated with RNA)
The nucleoside of uracil associated with RNA?
uridine (uracil not associated with DNA)
How many bonds between G and C pairs?
three, H-bonds
How many bonds between A and T or A and U?
2 H-bonds (A=T or A=U)
Are A,G,C,T, and U the only bases?
No, the are other minor bases in both DNA and tRNA
What kind of linkage do you see in RNA and DNA polymers?
phosphodiester linkage with 5' to 3' directionality...alternating sugar and phosphate groups form the a chain there is usually a phosphate at the 5' end but not the 3'
Which carbon is the phosphate usually attached to?
5'...but it can also be attached to 2' or 3'...and there are cyclic nucleotides with phosphate attached to C carbons, forming a ring (ex, cAMP)
Why is the backbone of DNA and RNA polymers considered hydrophilic?
a) because at physiological pH, each phosphate group is negatively charged

b) because of the free -OH groups in RNA
Explain the hydrolysis of the covalent backbone?
the covalent backbone is subject to hydrolysis...though this is a slow process...But under alkaline conditions (high pH) RNA is rapidly hydrolyzed...BUT DNA is not
What is the convention in writing DNA and RNA sequences?
with 5' (phosphorylated end) on left and 3' (not phosphorylated end) on right
Some different ways to write this nucleic acid sequence: ACGTA
pACGTA or see p 278 for schematic showing phosphoro on left and OH on right
The 3 key properties of the bases?
1. generally flat or close to it

2. maximum light absorbance is at 260nm

3. the bases are mostly hydrophobic at at physiological (near neutral pH)...this leads to [intra-strand] base-stacking)
What is base-stacking?
property of a nucleic acid...very imp. for their structure...bases are one on top of another because everything else around them is hydrophilic and they are hydrophobic...along with base pairing it is one of the two most important features for maintaining nucleic acid structure.
What are the two most important features for maintaining nucleic acid structure?
base stacking and base pairing
Base pairing?
inter strand or in RNA sometimes intrastrand is very important (H-bonding)
Watson and crick base pairs?
G(3 h bonds)C, A=T, A=U
The 3 levels of nucleic acid structure?
1. primary = sequence (just order)

2. secondary = local interactions and patterns (helix is most common)

3. tertiary = 3-dimensional, longer-range, possibly involving other mol.s
The predominant conformation of DNA? (secondary structure)
3-D Watson-Crick model of DNA

1. Right handed double helix

2. H-bonds between bases

3. Major and Minor grooves alternate

4. 2 anti-parallel strands
The outside of the watson-crick model is what?
the hydrophilic backbone (alternating phophoro-sugar-phosphoro..etc)
The inside of the Watson-crick model?
stacked bases...perpendicular to helical axis...paired
What is Chargraff's rule #4?
because G=C and A=T, A + G = T + C...for every G there is a C and same for A and T so A+G(purines) = T+C(pyrimidines)
What make DNA replication possible according to the Watson-Crick model?
unwrapping and wrapping of paired strands (daughter strands and parent strands etc)
The 3 forms of DNA?
1. A

2. B

3. Z
Describe the A form of DNA?
1. R handed like Watson and Crick

2. favored in absence of H2O

3. Wider than B

4. More compact than B

like a compressed spring (short and thick) compared to B
Describe B form of DNA?
watson and crick model
Describe Z form of DNA?
1. left handed

2. naturally occuring (found in some stretches of DNA)

3. narrower than B

4. more elongated than B

(like stretched spring)

Is A or Z found in lab?
A found in lab, Z found in life...A not yet seen naturally
Diameters of A vs. B vs. Z?
A = 26A

B = 20A

Z = 18A
Relative helix rise per base pair A vs B vs Z?
A = 2.6A

B = 3.4A

Z = 3.7A
Relative distance per turn A vs B vs Z?
A = 28

B = 36

Z = 44
In vivo what probably plays a role in determining whether a given segment of DNA exists in the B or the Z form?
the sequence of nucleotides
What is a palindrome?
if you turned and flipped it it would be the same (see notes very clear)
What is a mirror repeat?
just flip it (see notes very clear)
What secondary structure can palindromes form?
1. hairpins (stemloops) for single stranded

2. Cruciform for Double strand (looks like 2 hairpins)
Besides the 1 and 2 strand structures what else probably exists? Are they important?
there are also 3 and 4 strand structures found in nature...not common but may be very DNA/RNA drugs in development - combine with the body's DNA/RNA
What are Hoogsteen pairs associated with?
triple stranded DNA
What is H-DNA?
triple helix
What is mRNA?
messenger RNA
How is mRNA synthesized?
from DNA...transcription
What does monocistronic mean relative to mRNA?
piece of RNA with only one transcribed gene
In terms of mRNA what does polycistronic mean?
more than one gene
Prokaryotes can have what type of mRNA?
mono- or polycistronic
eukaryotes mostly have what type of mRNA?
monocystronic (this includes humans)
Since mRNA synthesized from DNA what can you say about it's structure?
right handed helix with base stacking
Describe tRNA?
transfer RNA....links mRNA and amino acids
Describe rRNA?
ribosomal RNA...the core of ribosomes (enzymatic role within RNA although they usually make new proteins)
What are some "other RNAs"?
viruses, ribozymes
The RNA is usually what structurally?
single stranded with hairpins, bulges, internal loops, and single folds back on self...imperfect regions....energetically favorable....looped and bulged regions are not part of the paired regions always
What can RNA from base pairs with?
self...or with other RNA or DNA...G(triple bond)C, A=U, and sometimes G=U
In it's double stranded regions what form does RNA most commonly exist in?
A form (in secondary structure)(RH helix, with base stacking)...B form not observed...Z form made in lab
in RNA their can be extensive what? What else is important?
can be extensive secondary structures...and tertiary structure is important (very specific)
What are ribozymes?
RNA enzymes
What is the denaturation of nucleic acids?
What is annealing of nucleic acids?
renaturation...tells us that the propensity to come together is inherent within each strand
How can you monitor denaturation and renaturation? Why?
UV absorption...because it varies as a function of base stacking and pairing, and so can be used to determine whether DNA is paired or denatured
When denaturation occurs which bonds break and which do not?
H-bonds break...covalent breaks do not
Where is the tm (melting point) for denatured DNA?
mid-point of a melting curve...different for different DNAs because they have different base concentrations
The more G + C DNA has the higher the what?
melting point because of H harder to pull apart...remember these have 3 would just look at a graph to figure it out
Which is more tightly bound RNA:RNA hybrids or RNA:DNA hybrids or DNA:DNA hybrids?
Where is hybridization important?
in research, medical diagnostic tests, and new drugs
Describe chemical transformations of nucleotides and nucleic acids?
1. nonenzymatic so very slow/rare

2. cause of mutations

3. 3 types of spontaneous rxns

a. Removal of exocyclic amine (deamination)

b. Breaking the sugar-base bond

c. UV irradiation (dimer formation)
Which chemical formations is caused by chemicals such as nitrites and nitrates (nitrosamines, HNO2) and bisulfites?
deamination : removal of exocyclic amines...replace it with O2
Which chem. transformation involves the breaking of a sugar-base bond?
depurination...mostly happens in cells where it doesn't matter
Which chm. transformation is caused by UV radiation?
dimer formation...mutates DNA, cancer...induced (not chemical)(light)
Some deaminating agents?
in some foods...nitrites, nitrates, nitrosamines...nitrous acid...bisulfite (preservatives) smoked foods
What are alkylating agents? ex.
reactive chm. that may cause nucleotide or NA transformations...disrupts base pairing...dimethylsulfate...add alkyl (-CH3)
What is an oxidative agent?
reactive chm. that may cause nucleotide or NA transformation...cells do have defense mechanisms against these
DNA methylation is what?
a specific type of DNA alkylation...sometimes happens naturally...can provide natural protection
What is important for the human genome project?
the sequences of DNA strands can be determined
2 methods for determining DNA sequences?
1. Maxam-Gilbert (degradative, breakdown)

2. Sanger (synthetic, build up)

3. human genome project
Can you synthesize DNA in the lab?
yes but only up to 70-80 nucleotides...not as long as human genes...can't create whole cells
How are nucleotides important in their own right? (stand alone functions)
1. energy carriers: ATP->ADP->AMP->adenosine

2. component of enzyme cofactors (coenzyme A, NAD, and FAD)

3. regulatory molecules (cAMP, cGMP, ppGpp)