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Biochem & Cell bio > Unit 8.2 > Flashcards

Unit 8.2 Flashcards

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Biology 101 flashcards
1
Q

What were Chargaff’s rules?

A
  1. base composition of DNA varies between species
  2. different tissues of the same species have the same base composition, regardless of age, nutritional state, or environment.
  3. %A = %T, %G=%C, %A + %G= %T + %C
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2
Q

Describe B-form DNA structure

A
  • Double right-handed (clockwise turn) helix
  • sugar-phosphate backbone points outward, bases on the interior
  • 20 A diameter
  • anti-parallel polynucleotide chains (5’ > 3’
    3’ > 5’ )
  • bases are nearly perpendicular to the axis
  • approx. 10 bp/turn, 3.4 A base separation
  • has major and minor grooves. proteins and other molecules to bind at the major grooves
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3
Q

What interactions stabilize the double helix?

A
  • Hydrogen bonds
  • Van der waals interactions (base pairing)
  • hydrophobic interactions
  • only if you have complementary bases. No complementary bases- no H-bonds= no double strand
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4
Q

How many H-bonds are formed between A&T, G&C?

A
  • A&T forms 2 hydrogen bonds
  • G&C forms 3 hydrogen bonds
    these pairs bond at the most stable angle for stacking
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5
Q

Why are hydrogen bonds not enough to stabilize the DNA helix?

A
  • Hydrogen bonds also competes in water
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6
Q

major groove side vs. minor groove side

A
  • proteins bind major groove side b/c it gives more information about what bases are present and what order compared to the minor groove side.
  • do not have to denature the protein to tell where the bases are
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7
Q

List the characteristics of A-form DNA

A
  • has C-3 endo deoxyribose shape
  • angles of the bases are tilted due to the C-3 endo shape.
  • more compressed than B-form
  • antiparallel chains
  • This form is seen when DNA is dehydrated/ crystalline, RNA-DNA hybrids, and RNA-RNA double strands
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8
Q

List the characteristics of Z-form DNA

A
  • uses C-2 endo shape for pyrimidines
  • uses C-3 endo shape for purines
  • a left-handed helix
  • zigzag backbone due to the alternating C-2 and C-3 endo
  • seen in vitro induced by high-salt concentrations. (high salt concentrations reduce repulsions b/w phosphate groups)
  • promoted by underwinding of DNA
  • anti for pyrimidines and syn for purines
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9
Q

List the alternate DNA structures and what they are supported by

A

Watson and Crick
1. Hairpins (1 side)
2. Cruciforms (both sides)

Hogsteen pairing
1. H-DNA (triplexes) has waston-crick pairing too
2. quadruplexes
3. tetraplexes

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10
Q

Most dominant form of DNA?

A

B-form

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11
Q

Compare DNA double helix to Protein alpha helix

A

DNA Double helix:
- the hydrogen bonds in the double helix are perpendicular to the helix axis.
-the double helix is flexible and bendable

Alpha helix
- hydrogen bonds in the alpha helix are parallel to the helix axis
- alpha helix is stiff and less bendable

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12
Q

Convert 1 kilobase pair to base pairs

A

1 Kbp = 1000 bp

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13
Q

What is a codon?

A

a sequence of 3 nucleotides in a DNA (or mRNA) that specifies a particular amino acid or termination of protein synthesis

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14
Q

What is complementarity?

A
  • each strand serves as a template for a new ‘daughter’ strand with a complementary sequence
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15
Q

what are the Biological consequences of DNA structure?

A
  • the base sequence provides a code for the storage and transmission of genetic information
  • the complementarity allows for the maintenance and transmission of information
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16
Q

What is DNA tertiary structure?

A
  • supercoiling
  • the double helix coils around the axis
  • this happens when there’s torsional stress
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17
Q

What are the reasons behind torsional stress in supercoiling of DNA helix

A
  • local unwinding
  • usually during replication
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18
Q

Where is DNA supercoiling seen?

A
  • in circular (or covalently closed) DNA
  • in linear DNA molecules with fixed ends
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19
Q

True or false. Most DNA in the cell is supercoiled?

A

True
- supercoil compacts the molecule
- it facilitates strand separation
- alters access of proteins

20
Q

What manages supercoiled DNA? and How do they do this?

A

Topoisomerases
- These are enzymes that convert one topoisomer to another
- these enzymes release or introduce torsional stress by cleaving and resealing the DNA strand
- can happen with single-strand or double-strand cuts

21
Q

What are the DNA supercoiling parameters?

A
  • Lk: linking number
  • Tw: twisting number
  • Wr: Writhing number
22
Q

define the linking number, twisting number, and writhing number.

A

Lk: the number of times a stand, when laying flat touches a surface.
- in relaxed DNA Lk= #bp / (#bp/turn)
- positive for right handed helix

Tw: # of twists or turns of the helix

Wr: the number of supercoils

23
Q

What happens when you unwind DNA helix causing torsional stress?

A
  • you get a negative superhelix
  • it’s the same number of bp, same sequence, but different degree of supercoiling
24
Q

relaxed DNA vs Highly coiled DNA on agarose gel

A
  • supercoils are highly compact and so DNA must be linearized to see how long they actual are.
  • linearizing the DNA decreases the linking number
25
Q

What is a nick?

A
  • A cut in DNA
26
Q

Type I topoisomerases vs. type II topoisomerases

A
  • type I
    • makes single-strand breaks to relax DNA/release supercoils.
    • involves reversible transesterification reactions
  • type II
    - makes double-strand breaks to release supercoils.
    - requires ATP for conformational change. not to cleave DNA
    - some introduce negative supercoils (e.g. bacterial gyrase)
27
Q

What is the clinical correlation for bacterial topoisomerases?

A
  • bacterial topoisomerases are targets for antibiotics.
  • bacteria cannot handle the torsional stress it cannot replicate
28
Q

What does Novobiocin do? What do Nalidixic acid and Ciprofloxacin do? Why is this important in cancer treatment?

A
  • novobiocin prohibits the taking of the second DNA strand
  • Nalidixic acid and Ciprofloxacin prevent the religation of the double strand. this causes a build-up in ds breaks in the bacteria leading to cell death.
  • important in cancer treatment because it leads to cell death during S-phase where replication occurs rapid for cancer cells.
29
Q

Describe the characteristics of RNA

A
  • contains Uracil, not thymine during de-novo synthesis
  • contains ribose, not deoxyribose
  • has lower chemical stability compared to DNA b/c of the 2’ carbon hydroxyl group that can react with a phosphate group
  • secondary structure is a single strand
  • local double-strand formation through stretches of base pairing
  • many different conformations possible
  • stability of the double helical regions are similar to DNA
30
Q

Describe RNA secondary structure

A
  • right-handed helix with base stacking in ssRNA
  • partial double-stranded secondary and tertiary conformations
  • secondary structures are antiparallel with conformation similar to the A-form of DNA
31
Q

what are common RNA secondary structures?

A
  • Hairpins
  • stem-loop
32
Q

What are common RNA tertiary structures?

A
  • pseudoknot (stem-loop)
33
Q

Can you calculate base percentages of RNA? why or why not?

A

You cannot calculate the base percentages of RNA because it is single stranded. It has to be calculated through chemical analysis

34
Q

What is denaturation?

A

the partial loss of secondary/tertiary structure

35
Q

What is renaturation?

A

reforming the secondary/teritary structure

36
Q

Hybridization vs. annealing

A

Hybridization is specific terminology for nucleic acids, it also means renaturation
annealing is the terminology used for binding a longer nucleic acid to a shorter one. but also means renaturation

37
Q

List the methods for denaturation/ disruption of noncovalent bonds

A
  • heat (most common)
  • extreme ph
  • certain chemicals in vitro
  • helicase (in vivo)
38
Q

ssDNA vs. dsDNA in spectroscopy

A
  • ssDNA absorbs more UV light than dsDNA because more base stacking in dsDNA
39
Q

What is hyperchromicity?

A

increase of UV light absorption in ssDNA or dsDNA

40
Q

What can be concluded from 50% denaturation?

A

the melting temperature (Tm)

41
Q

What determines melting temp?

A

Base composition:
- the # of non-covalent bonds present
- the more non-covalent bonds that have to be broken the higher the melting Tm
- the higher the G-C content the higher the melting temp
- can use the melting temp to figure out the G-C content

Length of template:
- more base pairs= more interactions
- 4C(#G+C) +2C(#A+T)

ion concentration
- ions reduce repulsive forces between phosphates, thus low ion concentration lowers Tm

pH extremes:
- protonation of bases at very low ph
- deprotonation of bases at very high pH

42
Q

What is the relationship between G-C content and melting temp (Tm)

A
  • linear relationship
  • directly proportional
43
Q

What are the means for denaturing nucleic acids?

A
  • increase temperature
  • H-bond disrupting agents (mostly used for electrophoresis)
    urea + formamide
  • Extreme pH at low temp
  • Low ionic concentration
44
Q

methods for renaturing/hybridizing nucleic acids

A
  • Decreasing temperature
  • Neutralizing pH
  • adjusting ion concentration
45
Q

Explain the significance of complementarity in reforming h-bonds

A
  • it does not matter what the source of the bases are (DNA, RNA, eukaryote, prokaryote, etc) as long as the bases are complementary they will reform hydrogen bonds

Biochem & Cell bio (20 decks)

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