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Intro to Med > DNA structure > Flashcards

DNA structure Flashcards

1
Q

What is DNA made up of and what bonds is each unit linked by?

A

DNA made up of nucleotides-
repeating base-sugar-phosphate units
linked by 3’-5-phosphodiester bonds

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2
Q

What base pairs is the DNA helix held together by?

A

DNA helix held together by AT and CG basepairs

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3
Q

What orientation are the 2 chains in DNA and what helix do they form?

A

Two antiparallel polynucleotide chains form a RH helix

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4
Q

What subunits are in the inside of the helix and what are on the outside for DNA?

A

Bases on inside of helix- phosphate and sugars on outside

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5
Q

What is the diameter of DNA and how many base pairs per turn in B-form>

A

Diameter 2 nm; ~10 bp per turn in B-form

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6
Q

What are the polynucleotide chains held together by in the DNA helix?

A

Polynucleotide chains held together by HYDROGEN BONDS between pairs of bases AT, GC

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7
Q

What form does tRNA fold in?

A

tRNA folds in an A-form helix

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8
Q

What are the 3 helical forms of DNA?

A
  1. A form
  2. B form
  3. Z form
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9
Q

What is left handed DNA detected in?

A

Can be detected in cells-favoured by high salt

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10
Q

What form of DNA predominates in nature?

A

B-form DNA predominates in nature

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11
Q

What is a tetraplex DNA?

A

A four stranded DNA helix formed at telomeres. Requires G-rich DNA sequences

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12
Q

What is a holliday junction:4-stranded junction DNA?

A

Arise naturally in living cells through DNA
strand exchange between two homologous
chromosomes- red and blue duplexes above.
Important role in DNA repair.

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13
Q

How can relaxed DNA be converted into supercoiled DNA?

A

-Conversion catalysed by Gyrase and ATP

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14
Q

What are the 4 levels of DNA structure?

A

1.Primary
2.Secondary
3.Tertiary
4.Quaternary

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15
Q

What is primary DNA structure?

A

sequence of bases (DNA sequencing

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16
Q

What is secondary DNA structure?

A

helical structure (X-ray and chemistry)

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17
Q

What is tertiary DNA structure?

A

DNA supercoiling (Electron microscopy)

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18
Q

What is quaternary DNA structure?

A

Interlocked chromosomes

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19
Q

How does sanger sequencing work?

A

A DNA strand is copied with a DNA
polymerase in the presence of
inhibitors that arrest DNA synthesis
specifically at A, C, G or T. The
DNA strands are separated by length
on a polyacrylamide gel. If the DNA
or incorporated inhibitor is
radioactive or fluorescent, the DNA
bands can be visualised and the
sequence read. 700-1000 bases per
read.

20
Q

how is bacterial DNA supercoiled and caused by what enzyme?

A
  • Is supercoiled- the DNA ribbon is itself twisted in space
  • Supercoiling caused by the enzyme DNA gyrase
21
Q

How is the DNA complex in eukaryotic cells and what does this form?

A

DNA is complexed with histones and other proteins to form a nucleoprotein complex- called CHROMATIN

22
Q

What is a nucleosome?

A

basic building block of chromatin

23
Q

Structure of nucleosome

A

-composed of a litlle less than 2 turns of DNA wrapped around a set of 8 proteins called histones, known as a histone octamer
-Histone octamer composed of 2 copies of each of the following histone protein:
-H2A
-H2B
-H3
-H4

24
Q

Hierachy of DNA coiling

A

DNA–>Beads on string–>30nm fibre–>Higher order coiling and looping–>Chromosomes

25
Q

How can DNA be damaged?

A
  • Spontaneous- e.g. loss of bases, or hydrolysis of C to U
  • Chemicals, and radicals generated by oxidative metabolism
    -change base structure- (but also cyclophosphamide)
    -insert between bases- (intercalators such as doxorubicin
    widely used as anticancer drugs)
  • Radiation
    -UV light produces thymine dimers
    -Ionising radiation (X-rays, gamma rays) break DNA
    chromosomes to cause leukaemia
26
Q

What does DNA repair maintain?

A

Maintains genome stability

27
Q

What is DNA replication

A

DNA replication is semiconservative, meaning one strand is the parent strand and the other is a new strand

28
Q

Where is DNA replication initiated?

A

DNA replication is initiated at specific sites on
DNA called replication origins

29
Q

What are replication origins recognised by?

A

Replication origins are recognised by an initiation complex

30
Q

What occurs at the replication origin and what phase of the cell cycle does DNA synthesis occur?

A

DNA at the origin unwinds to form a replication bubble and
allow access to the replication machinery
DNA synthesis occurs in a specific phase (S) of the cell
cycle and involves complete unwinding of the parental DNA

31
Q

Where does DNA replication initiate ate in eukaryotic cells?

A

In eukaryotic cells, DNA replication initiates at
multiple replication origins

32
Q

What catalyses the leading and lagging strand in DNA synthesis?

A

Replicative DNA polymerases catalyse leading and lagging strand synthesis in a multienzyme process

33
Q

What direction does DNA polymerase act in?

A

Acts in 5′ to 3′ direction- has important consequences.

34
Q

What does DNA polymerase utilise?

A

Utilises A-T and C-G base pairing to synthesise new DNA strand.

35
Q

What does DNA polymerase require?

A

Requires a DNA template, a DNA or RNA primer, the four
deoxyribonucleoside triphosphate (dNTP) building blocks
and Mg2+ ions.

36
Q

What important function does DNA polymerase have?

A

Has a proof-reading editing function

37
Q

What are the building blocks of DNA?

A

Deoxyribonucleoside triphosphates- building blocks for DNA

38
Q

What does DNA polymerase add?

A

Polymerase adds
a nucleotide- i.e. a
base-sugar-phosphate
to the 3’-OH end
extending the chain in
the 5′ to 3′ direction

39
Q

What do all known DNA polymerases add to the growing strand?

A

All known DNA polymerases including replicative
polymerases δ and ε add nucleotides to the 3′ OH end of the
growing strand. Thus, DNA synthesis always proceeds in
the 5′ to 3′ direction.

40
Q

What does the 5’ to 3’ activity of DNA polymerase mean for one DNA strand?

A

5′ to 3′ activity of DNA polymerase means the lagging DNA strand must be made discontinuously

41
Q

What are okazaki fragments?

A

Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

41
Q

What does topoisomerase do?

A

Topoisomerases remove +ve supercoils ahead of DNA replication forks-
solves the ‘DNA winding problem’

42
Q

How does DNA synthesis occur with high fidelity?

A

Base pairing in DNA, proof-reading by DNA
polymerase, and mismatch repair system ensure
DNA replication proceeds with high fidelity

43
Q

What inherited defects in humans causes colon cancer?

A

hMLH and hMSH

44
Q

What are examples of antibacterial agents that are gyrase inhibitors?

A

-Ciprofloxacin
-Levofloxacin
-Novobiocin

45
Q

What are the examples of antitumor agents that are TOPO II inhibitors?

A

-Etopside
-Doxorubicin
-Mitoxantrone

Intro to Med (46 decks)

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