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Biochemistry > Chapter 24-DNA/ RNA sructure > Flashcards

Chapter 24-DNA/ RNA sructure Flashcards

(68 cards)

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1
Q

What are the three major forms of DNA

A

A-DNA, B-DNA, and Z-DNA

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2
Q

Which DNA form is most common under physiological condition

A

B-DNA

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3
Q

What is the helix direction of A-DNA and B-DNA

A

both are right-handed helices

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4
Q

What is the helix direction of Z-DNA `

A

Left-handed

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5
Q

What is the sugar pucker conformation in A-DNA vs. B-DNA

A

A-DNA :C3’-endo , B-DNA: C2-endo

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6
Q

which form of DNA has a zig-zag shaped backbone

A

Z-DNA

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7
Q

Under what condition does A-DNA typically form

A

under dehydrated or low-humidity condition

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8
Q

In what type of molecule is A-DNA structure more commonly seen beside DNA

A

RNA-RNA and RNA-DNA hybrids ( dsRNA)

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9
Q

When might Z-DNA appear in cells

A

During active transcription of GC-rich regions or under high torsional stress

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10
Q

What are the major and minor grooves like in B-DNA

A

Major groove: wide and deep; Minor groove; narrow and shallow

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11
Q

How does the Z-DNA groove structure differ from B-DNA

A

Z-DNA has a flatted major groove and a deep narrow minor groove

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12
Q

Which DNA form is most stable

A

B-DNA is the most stable under physiological conditions

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13
Q

What is the biological significance of Z-DNA

A

may be involved in gene regulation and relieving torsional stress during transcription

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14
Q

Which DNA form is typically observed in crystal structures

A

A-DNA

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15
Q

What is DNA Supercoiling

A

The over or under winding of the DNA double heliz, which affects its compactness and function

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16
Q

What are the two types of DNA supercoling

A

posive supercoiling (overwound) and negative supercoiling (under wound)

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17
Q

Why is DNA supercoiling important

A

It helps compact DNA into the nucleus and regulates access for replication and transcription

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18
Q

What do topoisomerases do

A

Enzymes that regulate DNA supercoiling by cutting, rearranging, and rejoining DNA strands

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19
Q

What is the key difference between Type 1 and Type 2 Topoisomerase `

A

Type 1 makes a single-stand break; Type 2 makes a double-strand break.

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20
Q

Do type 1 of Type 2 topoisomerase require ATP
`

A

Type 2 is ATP-dependent

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21
Q

What is the role of type 1a topoisomerases

A

Relax negatively supercoiled DNA by cutting one strand and passing another single stand through

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22
Q

What is the role of Type 1B topoisomerases

A

Relax both positive and negative supercoils by allowing controlled rotation of the cleaved strand.

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23
Q

Does type1B form a covalent intermediate

A

Yes, but it forms a covalent 3’- phosphoserine intermediate.

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24
Q

What is the mechanism of action for Type 1B topoisomerases

A

cut one strand, allow it to rotate around the other strand to relieve super coils, then relegate

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25
What is the function of type 2 topoisomerase
Cut both stands of DNA, pass another double-stranded segment through the break, then reseal it .
26
How does Type 2 topoisomerase change DNA topology
it can introduce or remove supercoils, resolve knots, and untangle DNA
27
What are the major forces that stabilize the DNA double helix
Hydrogen bonding ( between complementary bases), Base stacking interaction ( Van der waals forces between adjacent bases ) Hydrophobic effects (bases are hydrophobic, shielded inside the helix) , Electrostatic interactions( negatively charged phosphate backbone repelled and stabilzed by cations like Mg+)
28
Which base pair contribute more to DNA stability
G-C because they form 3 hydrogen bonds and stack more tightly
29
What is DNA melting
The process of separating dsDNA into single strand by breaking hydrogen bonds
30
What conditions cause DNA to melt
High temperature, Alkaline pH, low salt concentration( destabilizes phosphate backbone shielding)
31
How can you reform DNA after it melts
Slowly cool the DNA to allow complementary strands to re-anneal through base pairing
32
What is DNA annealing
The reformation of hydrogen bonds between complementary DNA strands during cooling
33
What is a hyperchromic shift in DNA melting
an increase in UV absorbance (260nm) as DNA denatures
34
How is RNA structurally different from DNA at the nucleotide level?
RNA has ribose with a 2'OH group and uses Uracil
35
Can RNA from double Helices like DNA
yes, but they are usally short, right-handed A form helices, and often occur intra molecularly
36
What stabilizes RNA secondary structures
Bases pairing, Base stacking , and Hydrogen bonding and Mg2+ ions
37
How does RNA's 2' OH affect its structure compared to DNA `
the 2'OH group allows more hydrogen bonding and causes RNA to favor A-Form Helices, making it more flexible but also less stable then DNA
38
What are RNA secondary structures funcions
tRNA, rRNA( folding in ribosomes, ribozymes( cataytic RNA
39
How are RNA and DNA secondary sturctures similar
Both rely on watson-crick base pairing, base staking , and form helical regions
40
how are RNA and DNA secondary structure different
RNA is ss and forms complex 3D folds, DNA is ds with a uniform double helix and U or T
41
What are interactions in the context of biomolecules like DNA or proteins
interactions refer to non-covalent forces that hold molecules together or influence their shape and function, including hydrogen bond, ionic interations, hydrophobic effects, and van der waals forces
42
What is agarose gel electrophoresis used for
it separates DNA and RNA fragments based on size
43
How does agarose gel electrophoresis work
DNA is loaded into wells in a gel and an electric field is applied. DNA( negatively charged due to phosphate backbone) migrates toward the positive electrode.
44
What determines how far DNA travels in agarose gel
Smaller gragemtns move faster and travel farther, while larger fragments move slower and stay closer to the wells,
45
What is agarose, and why is it used for DNA gels
Agarose is a polysaccharide that forms a porous matrix; it's ideal for separating nucleic acids by size due to its consistent and tunable pore size
46
How do you visualize DNA in agarose gel
DNA is stained with dyes like ethidium bromide , which intercalate between bases and fluoresce under UV light
47
What is the role of loading dye in gel electophoresis
It helps you track the sample's movement, adds density so DNA sinks into the well, and typically contain colored dyes
48
What kind of interactions slow DNA movement through an agarose gel
Physical interactions between the DNA and the gel's mesh-like matrix-- larger DNA gets entangled more and moves slower
49
How is DNA packaged in eukaryotic cells
DNA is wrapped around histone proteins to form nucleosomes, then further coiled and looped into chromatin, eventually forming chromosomes during cell division
50
What is the basic unit of DNA packaging
The nucleosome, which consists of 147 bp of DNA wrapped around a histone octamer
51
What proteins make up the histone octamer in a nucleosome
Two each of H2A, H2B,H3, and H4
52
What is the role of histone H1
Histone H1 binds to the linker DNA between nucleosomes, helping to compact chromatin into higher-order structures.
53
What is chromatin
A complex of DNA and proteins( mainly histones) that organizes and compact DNA in the nucleus
54
How is the 30-nm fiber formed
Nucleosome coil into a solenoid or zigzag structure with help from histone H1, forming a fiber about 30 nm in diameter
55
How is chromatin further compacted beyond the 30-nm fiber
Through looping of the fiber onto a protein scaffold, forming chromosome loops, which then coil into chromosomes.
56
What post-translational modifications can histones undergo
Acetylation, Methylation, Phosphorylation, Ubiquitination
57
What is the function of histone modification
They regulate gene expression, DNA accessibility, and chromatin structure
58
What is a chromosome
A highly condensed form of chromatin that is visible during mitosis/meiosis, allowing accurate segregation of DNA
59
How much does histone-based packaging compact DNA
10,000 fold allowing 2 meters of DNA to fit into a 10 um nucleus
60
Where are histones genes found, and are they expressed all the time
Histone genes are clustered in the genome and are highly expressed during S phase for replication-coupled DNA packaging.
61
What are telomeres
they are repetitive DNA sequences (TTAGGG in humans) at the ends of linear chromosomes that protect them form degradation and fusion
62
What is the primary function of telomeres
They act as protective caps that prevent the loss of important gentic information during DNA replication and keep chromosome ends from being mistaken for broken DNA
63
Why do telomeres shorten with each cell division
Due to the end replication problem- DNA polymerase cannot fully replicate the 3' end of the lagging strand. So some telomeric DNA is lost with every division
64
What happens when telomeres become too short?
Cells enter senescence (stop dividing) or undergo apoptosis, contributing to aging and limited cell lifespan
65
What is telomerase
Telomerase is an enzyme that adds telomeric repeats to the ends of chromosomes maintaing telomere length
66
In which cells is telomerase active
active in germ cells, stem cells, and cancer cells, but usually inactive in most somatic cells
67
How are telomeres involved in aging
As telomers shorten over time in most somatic cells, it leads to reduced regenerative capacity and contributes to cellular aging.
68

Biochemistry (3 decks)

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