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Bchrm 413 Final Exam > 1 Nucleic Acid Structure > Flashcards

1 Nucleic Acid Structure Flashcards

(49 cards)

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1
Q

What is a nucleotide made of

A

Phosphate

5-carbon sugar

Nitrogenous base

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2
Q

What are the purines and pyrimidines

A

Purine : adenine and Gus in

Pyrimidines: cytosine, thymine, uracil

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3
Q

What does the sugar connect in the purines and pyrimidines

A

Pyrimidines: N1

Purine: N9

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4
Q

Structures of adenine and guanine

A

Adenine:

5 ring same (N CH NH C C)

6 C ring: 2HN-C C C N CH N C

Guanine:

5 ring same (N CH NH C C)

6 C ring: O=C C C N 2HN-C NH C

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5
Q

Where does H bonding happen on adenine and guanine

A

Adenine:

6 ring: 2HN-C N

Guanine:

6 C ring: O=C 2HN-C NH

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6
Q

Structures of thymine and cytosine and uracil

A

Cytosine:

NH2-C

CH

CH

NH

C=O

N

Thymine:

O=C

CH3-C

CH

NH

C=O

NH

Uracil:

Same as thymine , but no CH3-C

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7
Q

H binding thymine and cytosine and uracil

A

Cytosine: All three groups on left side

Thymine/URACIL: C=O and NH in left side (top 2)

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8
Q

What is the planarity of the bases

A

Pyrimidines planar

Purines very nearly planar

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9
Q

What are all of the base pairings

A

AT (DNA)

AU (RNA)

GC (DNA/RNA)

GU (RNA, wobble pair)

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10
Q

AT/U and GC base paring

A

AT/U:

NH2 and N on 6 c ring of adenine

Top C=O and NH OF T/U

GC:

Guanine: C=O, NH, c-NH2

Cytosine: c-NH2, N, C=O

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11
Q

Explain the GU base pairing

A

It’s a wobble pair

To base pair, the G and U need to be rotated, this is easier to do in RNA than dna which is why this happens in RNA

Doesn’t classify as having two h bonds, because of the rotation it equal to one hydrogen bond

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12
Q

Where does Wobble base pairing happen

A

Guanine: O=C, H-N

Uracil: NH and C=O (bottom c=O)

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13
Q

How many h bonds in each type of base pairing

A

A=T

G-U

G triple bond C

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14
Q

Explain ribose sugar structure (know how to draw)

A

Five c ring

O , OH UP, OH DOWN, OH DOWN, CH2 UP, OH attached to 5’ CH2

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15
Q

What type of ribose does DNA have

RNA

A

2-deoxyribose (not OH, H)

2-oxyribose (OH)

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16
Q

Where do the phosphates bind in the ribose sugar

A

5’ CH2 and 3’ OH

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17
Q

Explain the ribose pucker

A

The sugar is not planar so has pucker

C-2’ and C-3’ are either endo or exo (endo if facing up)

In DNA C-2’ is endo

In RNA C-3’ is endo because there’s more flexibility in RNA

Never exo

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18
Q

Where does the glycosidic bond happen

A

Bond between the sugar and the base

C1 of the ribose to N1 of pyrimidines or N9 of purines

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19
Q
A
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20
Q

What types of glycosidic bonds can purines and pyrimidines have

Study These Flashcards
A

Purines: syn (base facing in, can’t bp because can line of with other base pairs), or anti (base facing out can BP)

Pyrimidines: only anti because their C=O has too much steric hinderence if it faces in

In DNA purines are always anti form

To BP has to be anti

22
Q

Know how to draw sun or anti BP on sugar

23
Q

What is a nucleoside

What is are the nucleosides called in dna and rna

Study These Flashcards
A

Sugar + base

RNA:

Adenosine

Cytidine

Guanosine

Uridine

No thymidine since no thymine

DNA:

Same but with deoxy on all. (Deoxythymidine)

24
Q

What is a nucleoside also sometimes called

Study These Flashcards
A

Ribonucleoside

Deoxyribonucleoside

25
What makes up a nucleotide What bind makes the nucleotide
Nucleoside (sugar + base) + phosphate The phosphate is attached to the C 5’ of ribose via a PHOSPHOESTER bond (P-O-X) Could also be attached to the OH-C 3’
26
How would you name a nucleotide with adenine
Nucleoside name carbons attachement number of phosphates Not deoxy so RNA Adenosine 5’-monophosphate If deoxy: Deoxyadenosine 5’-monophosphate
27
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29
What are nucleotides in DNA and RNA linked together by
Phosphodiester bonds Meaning the phosphate has two ester bonds (one at 3’ and one at 5’ of sugar) The phosphate connects the 3’ C of one nucleotide to the 5’ C of the next nucleotide
30
What are strings of nucleotides called
Oligonulceotides (<50 bp) Or Polynucleotides (>50bp)
31
How are nucleotide sequences written
Like protiens that have an n and c term theyre writes 5’ to 3’ 5’-3’ or p-OH Because they have 5’ phos and 3’ oh
32
How is a double stranded helix formed What interactions stabilize this helix
When two polynucleotides come together Interactions: Interstrand: Base pairing between the two strands (h bonding), the two stand must be complimentary Intrastrand: base stacking interactions within the one strand, vanderwaals hydrophobic interactions
33
Can ds helix be parallel (both 5-3)
Yes but dsDNA is antiparallel (one 5-3 or 3-5)
34
35
DNA is a
Double stranded helix
36
What are the diffent ways the DNA can have different conformations
the bonds in the nucleotides affect the conformation of the helix: - Bonds 1,2,3 5,6,7 can rotate freely - But bond 4 in the ribose sugar has limited rotation , this cause the sugar pucker - Also the glycosyl bonds can be either anti or syn conf The helix could be left or right handed The two strands could be parallel or antiparallel
37
What are the three forms of DNA
A: right handed, c3 endo, anti glycosyl bond B: right handed, c2 endo, only anti glycosyl bond, antiparallel Z: left handed, pyrimidines c2 endo, purines c3 endo, anti for pyrimidines , sun for purines RNA is A form DNA is B form
38
What are the major and minor grooves of DNA
Major more accessible Also more distriguishable because all the base pairs al have diff h acceptor and donor profiles are the major groove which can be used to distinguish the grooves
39
What type of DNA do bacterial chromsomes and plasmid have Most DNA is ____ What is the effect of that
Circular double stranded Most dna is undercoiled, this allows access to the dna sequence Because most is undercoild, this causes dna torsional strain so the DNA supercoiled to compensate and relax the strain
40
What less stable, DNA or RNA and why
RNA because of the 2’ OH A base can attack that extra OH and cause cleaveage/degrade the RNA This is why we need to be more careful with RNA
41
42
What is the structur of RNA What are all of its forms
Single stranded tRNA, rRNA, ncRNA are all endogenous form of single stranded RNA They can form secondary structures like bulges, loops, hairpins If long enough, the hairpin from single stranded RNA can be dsRNA in the A form
43
What are the biologically important nucleotides
ATP adenosine cAMP DNA methylation
44
What is ATP
adenosine 5’ triphosphate (RNA molecule) Hydrolysis of ATP is used are a source of chemical energy in cellular reactions Since RNA mols wile you can’t use ATP to make dna, need dATP
45
What is adenosine
Found in important coenzymes (coenzymes A, NAD+, FAD+)
46
What is cAMP (Know how to draw)
adenosine 3’-5’-cyclic monophosphate Cyclic becuase is has a phosphodiester bond with itself An important second messenger in cellular processes
47
48
What is DNA methylation
Bacteria can methylate: - Adenine (6mA) and cytosine (4mC and 5mC) - this effects gene expression (epigenetics) - affects bacterial restriction modification systems (immunity) becuase Restriction enzymes cant recognize methylated DNA, don’t cut like they’re supposed to Eukaryotes can methylate: - Cytosine (5mC) - this effects gene expression (epigentics)
49
Why can’t restriction enzymes cut methylated dna
Major groove where it distinguish base pairs changes the profile when methylated so restriction enzymes cant recognize the methylated Methyl’s affect recognition of dna but not actual base pairing and helix

Bchrm 413 Final Exam (13 decks)

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