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1 - HB > DNA - structure and function > Flashcards

DNA - structure and function Flashcards

1
Q

What are nucleotides?

A

nucleotides join up to make nucleic acids
- 5 prime end joins to the 3 prime end and vice versa
- forms DNA or RNA depending on the sugar
are made up of
- a nitrogenous base = A, T, C, G or U
- a sugar = ribose (RNA) or deoxyribose (DNA)
- a phosphate molecule

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2
Q

How is DNA structured/arranged?

A

arranged in a double helix

  • helix is right handed
  • distance occupied by one complete turn of the helix is 34A which is equal to the distance of 10 base pairs
  • helix is not even = has major and minor grooves
  • strands are held together by interactions between bases = hydrogen bonds

purines (A,G) interact with pyrimidines (C, T and U)

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3
Q

What are the advantages of DNA structure/arrangement?

A

structure is stable

  • bases on the inside are protected
  • has high mechanical strength

easy to copy the strands
- template is always present

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4
Q

What are the different forms of DNA?

A

A form

  • shorter than the B form (initially described) = 28A
  • right handed
  • thicker
  • are RNA-DNA or RNA-RNA hybrids

B form

  • 34A distance
  • right handed

Z form

  • longer than A and B forms
  • left handed
  • thinner
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5
Q

How can DNA be packaged to reduce its size/length?

A

supercoiling

packaging in proteins

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6
Q

What are topoisomerases?

A

enzymes which cause changes in the degree of coiling
- introduce or eliminate coiling

topoisomerase II
- DNA gyrate = introduces supercoiling
topoisomerase I
- eliminates supercoiling

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7
Q

What is the difference in features of overwound and underwound DNA?

A

overwound = positive supercoiling

  • involves twisting towards the helical conformation = towards the direction the helix is already coiled/twisted
  • helix begins to distort and knot
  • increase in linkages on the helix

underwound = negative supercoiling

  • involves twisting against the helical conformation/direction
  • unwinds and straightens the helix
  • further helical stress can be removed by partial strand separation = hydrogen bonds break and part of the strand separates
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8
Q

How do organisms store their DNA?

A

DNA is stored in the negatively supercoiled form

  • decreases storage space
  • allows for easier opening of the helix = promotes DNA replication and transcription
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9
Q

How does topoisomerase I work?

A

cannot introduce supercoiling = does not use ATP

stimulates relaxation of the supercoiled DNA

  • reduces twists in the DNA strand
  • does not require ATP to function

cuts a single strand of the double helix and passes the other strand through it. it reseals and the helix forms with one less twist

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10
Q

How does topoisomerase II work?

A

introduces supercoiling

  • can introduce positive or negative supercoiling
  • requires ATP

cuts both strands of the double helix and passes a second DNA duplex (double strand) through the break then reseals the break
- can increase or reduce the linkage number by 2 units at a time

examples - DNA gyrase

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11
Q

How can DNA be packaged into proteins?

prokaryotes

A

has circular DNA

  • has superhelical domains that are separated by RNA or protein ‘locks’
  • DNA is highly condensed
  • is stored in a region of space called the nucleoid - fibrous structure

nuceloid

  • region where DNA transcription and replication take place
  • contains a combination of proteins

proteins bind to DNA and alter its shape and ability to replicate, recombine, repair
- proteins including Hu, IHF, Fis

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12
Q

How can DNA be packaged into proteins?

eukaryotes

A

has linear DNA

DNA must be compacted into nucleosomes to fit into the cell nucleus
nucleosomes
- segments of DNA wrapped around histone octamers (8 histones)
- are the smallest units of chromatin = chromatin condenses to form chromosomes

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13
Q

What are the types of chromatin?

A

euchromatin

  • are open and active
  • involved in active transcription of DNA to mRNA
  • stains lightly

heterochromatin

  • are closed and mainly silent = more tightly packaged and highly condensed so is not transcribed
  • stains darkly
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14
Q

How are nucleosomes formed?

A

formed DNA being associated with proteins = histones

histone octamer

  • is a 8 protein complex
  • contains two copies each of the histone proteins = H2a, H2b, H3 and H4

DNA wraps around the histone octamer to form nucleosomes
- are held together by H1 which is a linker protein = binds at the entry and exit regions of DNA, sits at the junction between nucleosomes and completes/holds together the nucleosome

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15
Q

What are the different types of DNA replication? What is the form that occurs in us? How can it be proven?

A

dispersive replication
- first and second generation daughter strands contain some of the new and old strand

conservative replication

  • first generation has one completely new and old strand
  • second generation has 1 old strand and 3 new strands

semi-conservative replication

  • first generation = each daughter cell has a single old and new strand
  • second generation = has two new daughter strands and 2 made of the old and new strands

Meselson Stahl experiment
- uses isotopes of nitrogen (14 and 15) to determine how the strands replicate

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16
Q

What is the process of DNA replication?

A

initiation

  • DNA is pulled apart at the origin = site of replication and is a fixed point in eukaryotes and prokaryotes
  • origin is recognised by proteins
  • direction of movement can be unidirectional (both strands replicate in the same direction) or bidirectional (strands replicate in opposite directions)

elongation
- catalytic reaction on the DNA polymerase which can only synthesis in the 5 to 3 prime direction

termination
- RNA primers are removed by RNase H enzyme

17
Q

How does the elongation section of replication occur?

A

DNA helicase unwinds the double stranded helix

  • begins at the origin and breaks the hydrogen bonds
  • forms the replication fork in the strands

DNA primase synthesises RNA primer to lay down a short stretch of 3 prime RNA for DNA polymerase to add on nucleotides
- in the leading strand DNA polymerase then moves and begins to add on nucleotides continuously = 5 to 3

  • in the lagging strand DNA polymerase attaches the nucleotides to the sections available
  • as DNA helicase opens more of the DNA strand and the replication fork progresses the DNA polymerase must constantly return to copy newly separated stretches of DNA = creates fragments
  • at each new fragment, a RNA primer must precede it to initiate DNA polymerase
  • removal of the primer by RNase H leaves gaps/nicks in the strands which must be fused together by DNA ligase
18
Q

Why is replication semi-discontinuous?

A

two strands of DNA are being replicated in opposite directions
- one strand is going from 5 prime to 3 prime while the other is going from 3 prime to 5 prime

leading strand
- goes from 5 prime to 3 prime = forms continuously

lagging strand
- does from 3 prime to 5 prime = forms discontinuously as DNA polymerase falls off synthesis the newly separated strands then the pieces are fused together

19
Q 
What is the role of in DNA replication?
DNA helicase
DNA polymerase 
primase
RNA primer 
DNA ligase 
topoisomerase 
single strand binding proteins
A

DNA helicase
- unzips/unwinds the DNA double helix by breaking the hydrogen bonds between bases

DNA polymerase

  • joins nucleotides together to form a new strand
  • adds the nucleotides onto the 3 prime end of the primer

Primase
- forms the RNA primer which initiates DNA polymerase

RNA primer
- form provides an attachment point for DNA polymerase which can only bond to 3 prime OH

DNA ligase
- joins/fuses together the okasaki fragments

Topoisomerase
- works at the region ahead of the replication fork to prevent DNA from being overwound (positive supercoiling) = can be overwound if DNA helicase pulls apart DNA which is fixed

Single strand binding proteins

  • protect single strand DNA during generation
  • stops it from being attacked by nucleases and prevents rewinding of DNA at the replication fork
20
Q

How is RNA primer removed from the newly synthesised strands?

A

can be removed by RNase H

  • enzyme
  • leaves nicks in the strands

can be removed by 5 prime to 3 prime exonucleases
- DNA polymerase I can be used to remove primers

21
Q

What is the processivity of DNA polymerase?

A

describes the polymerases activity
- describes the number of bases that DNA polymerase can synthesis in a single association with the template = without being released

processive polymerisation
- can synthesis a large number of bases = suitable for DNA replication = example is DNA polymerase III

distributive polymerisation
- can only synthesise a few bases at a time = suitable for DNA repair = example is DNA polymerase I

22
Q

What is the difference between 5 to 3 prime exonuclease activities and 3 to 5 prime exonuclease activities?

A

5 to 3 prime exonuclease

  • can remove primer
  • polymerase activity can fill nicks/gaps

3 to 5 prime exonuclease

  • used in proof reading or editing the DNA
  • can remove mismatched nucleotides/bases
23
Q

How can DNA be damaged endogenously and exogenously?

A

endogenous damage - inside the cell

  • replicative errors = incorrect bases, insertion, deletion
  • oxidative damage by free radicals
  • spontaneous alteration
  • alkylating agents

exogenous damage - damage from outside

  • UV
  • pollution
  • carcinogens
  • radiotherapy
24
Q

How are error in DNA dealt with?

A

direct reversal
- damaged area is repaired directly, does not require nucleotide template

nucleotide excision repair (NER)

  • error is removed as a stretch of nucleotides
  • typically done by UV damage

base excision repair (BER)
- only the affected base is removed

mismatch repair

  • mismatched bases = similar to NER
  • removes whole stretch of nucleotides

recombination repair

  • repairs double strand breaks
  • uses sequence from homologous pieces of DNA = occurs during S phase

non-homologous end joining (NHEJ)

  • joins ends of DNA even if they are not related/homologous
  • proteins brings the ends together then DNA ligase joins them

1 - HB (23 decks)

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