Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Molecular Biology > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

(69 cards)

Start Studying
1
Q

name four weak interactions in biological systems

A

h bonds
ionic bonds
van der waals bond
hydrophobic interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Not weak e- shared energy stored 50-150 kcal/mol

A

covalent bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q
  • weaker bonds that have important roles in molecular structure and stabilization
  • can be formed or broken, allowing flexibility for function
A

non covalent bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what happens if van der waals radii become close and not too close?

A

atoms that come close to van der waals raddi are strongly repulsed and not too close atoms may be weakly attracted to each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

ionic interactions have ____ chemical groups

A

charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

interaction due to partial charge resulting form a polar covalent bond

A

h bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

hydrophobic interactions drive _________

A

protein folding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

regions associate with one another and exclude water

A

hydrophobic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

reigions located outside surface of molecule where they can interact with water

A

hydrophilic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what charge is water considered?

A

partially charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

nucleotide vs nucleoside

A

nucleotide- consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups

nucleoside- consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

purine vs pyrimidine

A

purine- adenine and guanine (two C rings)

pyrimidines- cytosine, thymine, uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

deoxyribose vs ribose

A

deoxyribose- H at carbon 2 position

ribose- OH at carbon 2 position

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what position is associated with phosphodiester bonds in purines and pyrimidine?

A

purines- NH at position 9

pyrimidines- NH at position 1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

when is a pH protonated and unprotonated

A

protonated- pH below pKa

unprotonated- pH above pKa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

DNA and RNA polymers of nucleotides are written in the ________ direction

A

5’-3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q
  • molecule in which a p+ has migrated to a different place
  • interferes with h bonds but doesn’t change shape but may change variation
  • implications for the accuracy of DNA replication and can therefore provide genetic variation
A

tautomer or tautomeric isomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

in the human genome, along with 3 billion base pairs there are also ________ tautomers

A

100,000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

describe rare imino forms of adenine and cytosine

A

normal base pairing is C-G and A-T from watson- crick

this form changes base pairing, C is now with A

a double bonded N to C between A-C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

describe rare enol forms of thymine and guanine

A

normal base pairing is C-G and A-T from watson- crick

this form changes base pairing, G is with T

a single bond of O to H, closest to methyl group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

describe the structure of DNA

A

non-covalent H bonds to form double stranded DNA

complimentary Watson-Crick base pairs

  • A and T (2 h bonds)
  • C and G (3 h bonds)- harder to break

strands are antiparallel (5’ phosphate to 3’ sugar)

Per one turn

  • 10.5 bases per turn
  • 3.4 Angstrom rise (0.34 nm)
  • 2.0 nm wide

generally right handed double helix (B-DNA)
-interior stacking with h bonds and van der waals to stabilize
-base stacking is very energetically favorable and important fro stability of DNA
-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

right handed helix but has 11 bp per turn, making the grooves more evenly sized

this conformation can be included by DNA binding proteins

major groove: deep and narrow

minor groove: shallow and broad

conditions: low humidity (75%) high salt

A

A-DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

how can B-DNA form into A-DNA

A

DNA binding proteins, low humidity, high salt

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

left handed helix

can result from methylation of cytosine, torsional stress and high salt [ ]

major groove: shallow, virtually nonexistent

minor groove: very deep and narrow

bases per turn: 12

conditions: high MgCl2, NaCl or ethanol

A

Z-DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
what is the height of the hole and bases in DNA
3. 4 A base height | 2. 7 A hole height
26
what happens if water has access through the hole of DNa
hydrolysis (breaks strand)
27
describe DNA stabilization
-stacking causes hydrophobic interactions to stabilize structure
28
describe G-C content in DNA
increasing temp breaks DNA ( hi G-C content needs more higher heat to break A=T, G=C AT does not = GC GC is generally 50% but extremely variable and not uniform in genomes GC slightly denser (3 bonds) - high GC DNA moves further in a gradient - harder to separate generally more stable (useful for PCR)
29
how is DNA denatured and observed
denatured by heating observed by absorbance measurements (DNA abs is at 260nm)
30
which is larger: genomic or plasmid DNA
genomic larger than plasmid
31
name the Absorbances for dsNA, ssDNA and RNA, ss oligos
dsDNA A260= 1.0 for 50ug/mL ssDNA and RNA A260= 1.0 for 40ug/mL ``` ss oligos (tiny pieces of RNA) A260= 1.0 for 33ug/mL ***hyper chromatic shift ```
32
name the absorption ranges fro DNA and RNA
DNA: 1.8-1.9 (260nm/280nm ratio) RNA: 1.9-2.0
33
describe melting temp in DNA and RNA
DNA -temp at which 1/2 of DNA sample is denatured RNA -doesn't have melting temp bc its already ss
34
hydrogen bonds between the paired bases in the double helix limits the resonance behavior of the aromatic ring of the bases which results in decrease in the UV absorbance of dsDNA
hyperchromatic
35
importance of Tm
critical importance relies on complementary base pairing - designing PCR primers (know Tm) - Southern blots (DNA) - Northern bolts (RNA) - colony hybridization (targeting cells/tissues)
36
factors affecting Tm
- GC content of sample (more GC higher Tm) - presence of intercalating agent (anything that disrupts h bonds or base stacking) - salt concentration (hi salt can break H bonds in DNA) - pH (DNA is stable at pH of 8) - length- longer DNA length, higher Tm
37
structure associated with tandem repeats slipping during replication bubble structure forms but repair mechanism cuts it out
slipped structure
38
structure associated with palindromes and negative super coiling
cruciform structure
39
structure associated with transcription and mirror repeats watson-crick duplex associates w/ third strand through hoogsteen pairing
triple helices structure
40
restriction enzymes recognize _____
palindromes
41
describe triple helices structure
- third strand of DNA joins the first two to form triplex DNA - favored by purine-pyrimidine stretches with mirror repeat symmetry -Hoogstenen + Watson-Crick structure purine bases flip (A and G)
42
describe supercoiling
- closed circular DNA can be super coiled - supercoiled DNA is under tension and twists upon itself - open, uncoiled circular DNA is in relaxed form (O)
43
what breaks supercoiling?
topoisomerase
44
bacterial benefits of supercoiling
more compact so it fits in nucleoid
45
describe supercoiling
to induce supercoiling, a circular molecule is cut and held at one end while the other end is twisted this changes the number of bases per tune when the two ends are stuck back together (ligated), the DNA twist to restore preferred number of bases per turn this causes DNA to wrap around itself in a coiled structure
46
clockwise winding of DNA tending to separate the strands leads to ________
neg supercoiling
47
twisting in counterclockwise direction leads to _____
pos supercoiling
48
how can linear pieces of DNA be supercoiled
if one end is immobile
49
two ways supercoiling can be presented
toroidal (wrapped around a protein) interwound (similar to infinity shape)
50
number of times one strand of duplex DNA wraps around each other
linking number (Lk) to calculate: total bp of plasmid divided by 10.5 bases per turn (pitch) Lk= Tw + Wr
51
what is the pitch of DNA
10.5 bases per turn
52
represents the number of turns in a fragment of DNA a positive number= positive supercoiling a negative number= negatively supercoiling
twist (Tw) often similar to linking number
53
describes the supercoiling
writhe (Wr)
54
what is the writhe of a relaxed supercoil
wr=0
55
duplex RNA- A form bc of _______
2'-OH can facilitate the cleavage of phosphodiester bonds
56
RNA structure form, # bp per turn, pitch
A-DNA (wider and flatter right hand helix) 11. 0 bp per turn pitch: 30.9 Angstroms
57
describe RNA's possible secondary structure
stem loop - stem can contain watson-crick pairs, non canonical pairs (G paired with U, not normal; okay to have since its in the wobble position), or mismatched (will cause a bump) - loop- no pairing occurs bulge loop internal loop multi-branched loop stem loop
58
factors affecting tertiary structures in RNA
unusual bases, coaxial stacking, 2'-OH interactions, unusual h bonding *****folding often mediated by proteins (ex: rRNA)
59
part of RNA creating a duplex most common triple pairing w/ C and G minor groove of an Adenine inserts in the minor groove of a neighboring helices
A-minor motif
60
describe pseudoknot due to coaxial stacking
at least 2 stem-loop structures in which half of one stem is intercalated b/t the 2 halves of another stem crossing over occurs
61
why is there often more than one area of coaxial stacking
bc we tend to see more and one plane
62
pairing between GU not typical to watson-crick pairs base is often modified and can cause distortions 2 H bonds can occur from folding bulky distortion makes it hard for proliferation and can be bad if undetected
non- canonical pairs
63
what types of RNA regulate gene expression
small nucleolar RNA (snoRNA microRNA (miRNA), siRNA ribozymes
64
RNA-protein interactions can influence the ________ activity of proteins
catalytic
65
catalytic RNA can work alone or with proteins
ribozymes
66
therapeutic application of ribozymes
gene silencing
67
describe RNA structure and function
- forms complimentary bp with other nucleic acids - less restricted to standard WC bp - tertiary structure is less constrained bc ss - has a wider repertoire of bases than DNA - can interact with protein (ribonucleoprotein particles- RNP)
68
describe behavior of acids in nucleic acids
depurination- intermediate acid conditions depyrimidation- harsher treatment cleave of phosphodiester bonds higher in depyrimidation than depurination
69
describe behavior of bases in nucleic acids
N-glycosidic bonds stable in mild alkaline conditions DNA melts phosphodiester linkages in DNA and RNA show very different behavior in weak bases RNA linkages break bc of 2'-OH group

Molecular Biology (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions