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Molecular Biology > DNA Structure And Topology > Flashcards

DNA Structure And Topology Flashcards

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1
Q

Why is DNA central to life?

A
  • genomes of organisms contain information to construct and maintain a living organism.
  • DNA stores genetic information in a stable manner/encode information for various characteristics
  • DNA duplicates genetic information/accurate replication
  • DNA participates in regulating its own expression
  • DNA participates in regulating evolution/mutability
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2
Q

What is the transcriptome?

A

RNA copies of the active protein-coding genes

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3
Q

What is the proteosome?

A

The cell’s repertoire of proteins

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4
Q

Describe Mendel’s discovery

A
  • Gregor Mendel researched (1865) with garden peas and discovered that some ‘factors’ were arranged into packets of information that separated during gametogenesis
  • Mendel’s genetic ‘factor’ (now called ‘gene’ - a term coined since 1909 by Wilhelm Johannensen) is responsible for heredity
  • Mendel’s discovery revealed the inherent nature of genes
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5
Q

What question arose after Mendel’s discovery?

A

‘Where were these ‘factors’ located in the cell?’

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6
Q

Describe DNA was discovered for the first time

A

-In 1869, Johann Fruedrich Miescher, a Swiss biochemist, isolated what he called “nuclein” first from white blood cells and next from salmon sperm, a substance containing both phosphorus and nitrogen

Nuclein later became known as nucleic acid in 1874 when Meischer isolated protein and acid molecule from the nucleus

Nuclein now known as nucleic acid-DNA

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7
Q

What molecule is the carrier of hereditary information - protein or DNA?

A
  • After Friedrich Meischer’s isolation of “nuclein” and proteins from the nucleus (1874), the question was: which if these carry hereditary information?
  • at the time it was believed to be proteins but is most known it is DNA
  • Griffith’s transforming factor proved DNA was the carrier of hereditary information
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8
Q

What is Griffith’s ‘transforming’ factor?

A

Rough and smooth strains of Pneumococcus

  • Gelatinous capsule surrounds bacterium and protects it from the defense mechanisms of the infected animal, Smooth colonies cause disease
  • Some strains are unable to synthesize the capsule, they form small colonies -Rough colonies don’t cause disease.
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9
Q

How was Griffith’s ‘transforming’ factor used to experimentally show that DNA is the hereditary carrier protein ?

A

Frederick Griffith(1928) -trying to develop a vaccine against the pneumonia causing bacteria (Diplococcus pneumoniae)

  • Virulent bacteria retrieved from blood of the dead mice
  • mice injected with mixture of heat-killed virulent smooth strain and the live nonviruleht rough strain- mice died
  • mice died, Griffith reasoned that the “transforming factor” was transferred from the Heat killed to the non virulent bacteria.
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10
Q

What are the discovery of Avery and co.?

A

Destruction of dna prevents transformation

  • DNA is the transformation factor
  • heat killed virulent (no longer virulent) containing the transforming factor
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11
Q

What did Martha Chase and Alfred Hershey discover?

A

They used bacteriophage as a tool to prove that
-DNA is the genetic material

-Proteins don’t carry hereditary information

Note: bacteriophages (phages) are viruses that can infect bacteria

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12
Q

Explain the Hershey-Chase experiment with bacteriophage

A
  • Proteins and DNA of phages labeled with radioactive isotopes of sulfur and phosphorus respectively
  • phages used to infect Escherichia coli cells
  • Solution of Bacteria + phages agitated and centrifuged
  • Supernatant (containing the phage coats ) was rich in 35S
  • Subnatant or “pellet” (containing the bacteria + phage genes) was rich in 32P

Hershey and Chase therefore concluded that DNA contained he hereditary material

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13
Q

How did Erwin Chargaff form his rule?

A

Erwin Chargaff discovered that the makeup of DNA differs from one species to another

  • He also studied the ratios of bases in the DNA of different species and showed that:
  • the two bases adenine(A) and thymine (T) appeared in relatively equal amounts. So also guanine (G) and cytosine(C)
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14
Q

Explain Chargaff base pair ratio experiment

A
  1. DNA extracted and purified
  2. Acid hydrolysis to break down phosphodiester bond and release nucleotides
  3. Nucleotides quantified by chromatography
  4. 50% purines (A & G) and 50% pyrimidines (C & T)
  5. A=T (A pairs with and is equal in amount to T)
  6. G=C (G pairs with and is equal in amount to C)
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15
Q

What vital clues to DNA structure did Rosalind Franklin reveal?

A

X ray patterns, obtained by Rosalind Franklin revealed:
-The symmetry

  • Consistency in the structure of DNA
  • Vital clues about its dimensions
  • Franklins X-ray diffraction images confirming the helical structure of DNA were shown to Watson without her approval or knowledge
  • The rules of the Nobel prize forbid posthumous nominations
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16
Q

How was the molecular structure of DNA unveiled?

A

Watson and Crick saw Rosalind Franklins data without her knowledge and used to make a model of DNA

The men won rye Nobel prize in physiology or medicine 1962- “for their discoveries of the molecular structure of nucleic acids and its significance for information transfer in living material”

-Rosalind Franklin died from ovarian cancer before the prize was awarded and her contribution is often overlooked

17
Q

How did Watson and Crick deduce the double helical structure of DNA?

A
  • X-ray diffraction pattern of Franklin
  • the base ratios of Chargaffs rule
  • Biophysical data, e.g.the water content of DNA fibers
  • Scale Model building
18
Q

DNA is…

A

A polymer of nucleotides

19
Q

Describe different confirmations of the DNA double helix

A
  • Chromosomal DNA is thought to consist mainly of B-DNA
  • A-form when slightly dehydrated
  • Z form can naturally occur in regions of DNA that have alternating purines and pyrimidines like GCGCGCGC or ATATATATATAT
  • Transitions between B and Z form thought to play a role in regulating gene expression
20
Q

What are the features of B-DNA?

A

Right handed

Helical diameter (nm)=2.37

10 base pairs per complete turn

21
Q

What are the features of A-DNA?

A

Right handed

Helical diameter (nm)= 2.55

11 base pairs per complete. turn

22
Q

What are the features of Z-DNA?

A

Left-handed

Helical diameter(Nm)= 1.84

12 base pairs per complete turn

23
Q

What is DNA Supercoiling?

A
  • Many cellular DNA exist as long, thread-like closed circular double stranded molecules. E.g. bacterial and viral DNA
  • A coiling of such circular DNA molecule around itself results in a secondary coil known as Supercoiling
  • positive coiling
  • negative coiling
  • Almost all cellular DNAs, including linear DNAs (e.g. in eukaryotes) are negatively supercoiled
24
Q

What are topoisomerases?

A

The enzymes that regulate the level of Supercoiling of DNA molecules are called topoisomerases

25
Q

What are intercalators?

A

Can alter the geometry of the supercoiled molecule

-Ethidium bromide is a good example of an intercalator. It is positively charged and inserts itself between the base pairs thus binding to the DNA and causing a local unwinding of the helix by about 26 degrees

26
Q

Describe DNA packaging in prokaryotes

A
  • In prokaryotes, the entire genome is typically a single, closed-circular DNA molecule packed into the nucleoid
  • One way prokaryotes compress their DNA into smaller spaces is by Supercoiling

Circular, double stranded DNA —> removes a few turns of the double helix —> molecule forms a negative supercoil

27
Q

What role do proteins have in condensing prokaryotic DNA?

A
  • multiple proteins act together to fold and condense prokaryotic DNA e.g. HU proteins
  • HU proteins in E. Coli forms a tetramer wound with about 60 bp of DNA there are about 60,000 HU proteins per E. Coli cell.
28
Q

Summarize Eukaryotic DNA packaging

A
  • Nuclear DNA is so large that to be successfully packed into the tiny nucleus of cells, it is organized into physical structures called chromosomes
  • All eukaryotes have elaborate ways of packing DNA into chromosomes
29
Q

Describe the quaternary structures of DNA

A
  • In eukaryotes, linear DNA is complexed to histones (proteins) to form highly dense structures often referred to as a quaternary structure
  • Chromosomal DNA just under 0.05 m in length is packed into chromosome of length 1 to 10 um
30
Q

What are the levels of packaging of quarter are structure of DNA?

A
  • nucleosomes
  • loops of fibers (or beads on a string)
  • 30 nm fibers
31
Q

Describe the structure of a nucleosomes

A
  • basic units of Eukaryotic chromosome structure
  • four pairs of protein monomers (H2A, H2B, H3 and H4) make up the histone core (octamer)
  • The nucleosomes core particle consists of a histone octamer and about 146 base pairs of DNA
  • Each nucleosome is made up of a core particle plus histone (H1) and linker DNA
  • Linker DNA consists of about 54 base pairs
  • histone H1 binds to the core particle and to linker DNA
32
Q

Describe the ‘beads on a string’ packaging of DNA

A
  • This represents the next level of DNA packing
  • Beads= core nucleosome
  • String= DNA
  • Nucleosomes are connected together by linker DNA and histone (H1)
33
Q

Describe the 30nm fiber packaging of DNA

A
  • Nucleosomes can associate with each other through interactions b/w histone H1 to form a more compact structure (chromatin fiber)
  • Packed on top of one another, generating a regular array
  • the resulting fiber is about 30nm in diameter
  • Makes DNA even more highly condensed
34
Q

Explain DNA packaging in eukaryotes

A
  • DNA is wound around histone proteins to form the nucleosome
  • Several nucleosomes are linked together to form beads-on-a-string
  • Beads-on-a-string are further complexed to form the 30 nanometer fiber (solenoid)
  • Solenoid is further compacted to form beads-on-a-string
  • Chromatin loops are compacted to form a bottle brush configuration (rosettes of chromatin loops) which coil up further into the chromatids in chromosome

Molecular Biology (24 decks)

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