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Biochemistry > Nucleic Acid L2 > Flashcards

Nucleic Acid L2 Flashcards

1
Q

DNA = deoxyribonucleic acid

EXPLAIN

A
  • polymer of deoxyribonucleotides,
  • nt = nucleotide
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2
Q

WHAT JOINS THE SUGARS AND PHOSPHATES IN DNA?

A

PHOSPHODIESTER bonds join sugars & phosphates

5’ TO 3’

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3
Q

Explain the DNA PRIMARY STRUCTURE

A
  1. Sugars’ carbons are designated 1’,2’,3’,4’,5’
  2. BASE joins to the 1’ carbon
  3. PHOSPHATE to the 5’ carbon
  4. NEXT nt to the 3’ carbon
    So DNA has a 5’ and 3’ terminus
    (like proteins have ‘ends’)
  5. In DNA, ribose lacks O at 2’ carbon, hence DEOXY!
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4
Q

What does phosphate groups?

A

Note phosphate groups
“bridge” 3’OH of one nt
to 5‘C of next nt =
phosphodiester bond

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5
Q

Explain why is DNA is an ACID?

A

Phosphate groups
ionised (pKa low),

  • so carry negative
    charge at physiological pH
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6
Q

Is the “backbone” of DNA hydrophobic or hydrophilic?

A
  1. Covalent “backbone”
    of DNA is hydrophilic.
  2. Consists of alternating
    sugar-phosphates.
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7
Q

Writing Conventions: NA sequences

A
  1. Bases symbolised by first letter, A,C,G,T, U in RNA
  2. Phosphate groups are symbolised P which circled
  3. ALWAYS write NA in 5’ to 3’ direction
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8
Q

Sequence of <50 nt = ?

A
  1. Sequence of <50 nt = oligonucleotide (oligo)
  2. Longer = polynucleotide
  3. Even longer = nucleic acid
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9
Q

What is the structure of DNA?

PRIMARY VS SECONDARY STRUCTURE?

A
  • Like protein structure, it is useful to describe NA
    structure in terms of hierarchical levels of complexity:
  1. PRIMARY STRUCTURE = sequence of nts from 5’ to 3’
    e.g., ATCGTTTACAT, etc.
  2. SECONDARY STRUCTURE of DNA involves TWO STRANDS running ANTIPARALLEL, DEVELOPMENT OF MOFEL EXPLAINS:
    - Chemistry
    - Physical measurements
    - DNA’s ability to carry genetic information
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10
Q

Chemistry (& Chargaff) OF DNA = 6

A
  1. HYDROPHOBIC BASES , & HYDROPHILIC CHARGED
    BACKBONE OF PHOSPHATES AND SUGARS
  2. All DNA contains SAME AMOUNT OF PHOSPHATE,
    PENTOSE SUGAR, BUT DIFFERENT AMOUNTS OF BASES.
  3. ALL DNA, regardless of species, shows that:
    SUM OF PURINES = SUM OF PYRIMIDINES , A+G = T+C and amount of A = amount of T, & C = G …
  4. Exact base composition varies with species
  5. Base composition of DNA from different cells in a specimen is identical
  6. Base composition does not change with age,
    nutritional status, environment,
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11
Q

Physical Measurements

A
  1. X-ray measurements show regular structure:

Helix with complete turn every 3.4nm, diameter ± 2nm.

Density measurements: Helix must have TWO chains.

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12
Q

DNA as a Carrier of Genetic Information

A

TRANSFORMATION

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13
Q

DNA as a Carrier of Genetic Information:

What caused the change from a nonlethal R strain to the lethal S strain?

A
  1. DNA from the ruptured S strain cells was transferred to the R strain.
  2. This process is TRANSFORMATION, uptake of DNA from outside the bacteria, that integrates into the bacterial cell’s chromosome.
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14
Q

Bonds in the Double Helix:

A
  1. Watson & Crick proposed 2 POLYNUCLEOTIDE CHAINS COULD ASSOCIATE BY HYDROGEN BONDING BETWEEN BASE PAIRS.
  2. Hydrogen bonds:
    HYDROGEN atom
    shared between TWO
    OTHER ATOMS, BOTH
    ELECTRONEGATIVE
    (such as O & N)
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15
Q

Understanding Hydrogen Bonds in DNA….

A
  1. Hydrogen bonds are STRONGEST WHEN THE THREE ATOMS ARE IN A STRAIGHT LINE …..
  2. The bases in DNA hydrogen bond to form specific pairs known as COMPLEMENTARY BASE PAIRS:
    A with T and C with G
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16
Q

Explain Hydrogen bonds form between
complementary bases

A

A=T and G=C
A purine with a pyrimidine
A large base with a small

17
Q

Are Other Pairings Possible?

A
  1. Two fully extended chains could form H-bonded base
    paired complex - essentially a STEP LADDER STRUCTURE

2.BUT this is ENERGETICALLY UNFAVOURABLE - hydrophobic planes of bases prefer to be in closer contact with
each other rather than with water

18
Q

Double bonds of bases make pyrimidines & purines EXPLAIN

A

(nearly flat) planar …

In water, hydrophobic groups cluster together …
“hydrophobic interactions”

Such hydrophobic interactions
(stacking), as well as van der Waals forces & dipole-dipole interactions stabilise 3-D structure of nucleic acids.

This minimises contact with water

19
Q

Remember, H bonds between complementary
base pairs also stabilise the DNA double helix.

A

Remember, H bonds between complementary
base pairs also stabilise the DNA double helix.

20
Q

Explain The DNA structure:

Protein Interact where?
Bases project?
2 strands held together by?
Orientations of the 2 strands are…?
Strands are …?

A
  1. The sugar -phosphate
    backbone is on the
    outside (proteins interact).
  2. The bases project into the inside of the double helix.
  3. The two strands are held
    together by many
    hydrogen bonds &
    hydrophobic interactions
    between bases.
  4. The orientations of the
    two strands are
    antiparallel: 5’
    -3’ directions are opposite.
  5. Strands are
    complementary:
    C=G, A=T
21
Q

Helix is held together mainly by two sets of forces:

A
  1. H-bonding between base pairs &
  2. hydrophobic
    “stacking” interactions of bases.
22
Q

explain the Structure of the HELIX? = 4

A
  1. Specificity that maintains base sequence is contributed entirely by H BONDING BETWEEN COMPLEMENTARY BASE PAIRS.
  2. BASE STACKING increases DNA STABILITY.
  3. ‘10 bases’ make a COMPLETE TURN in the Watson-Crick
    model.
  4. A ‘RIGHT’ -handed helix with a MAJOR AND MINOR groove.
23
Q

What are the Grooves of the Helix?

A
  1. The helix
    has a WIDE & a NARROW groove
  2. Grooves ALLOW IONS & PROTEINS to INTERACT WITH DNA.
24
Q

What about the Helix?

A
  1. An EXTENDED STEP LADDER can be CONVERTED to A HELIX by A SIMPLE TWIST.
  2. Bases are STACKED NEATLY ON TOP OF ONE ANOTHER IN THE DOUBLE HELIX, GIVING A CONSISTENT DIAMETER TO THE HELIX… CELL CAN DETECT CHANGES.
25
Q

DNA in the Cell

A
  1. B FORM OF DNA MOST STABLE UNDER PHYSIOLOGICAL CONDITIONS.

——-Two other variants have been
identified in the lab, A & Z forms:

  1. A FORM is favoured in solutions devoid (almost) of water, so not our cells.
  2. Z FORM is a “ZIGZAG”, there is evidence short tracts of DNA can take on this shape in cells.
26
Q

DNA is flexible EXPLAIN….

A

DNA has several configurations.

There is rotation around the sugar-base bond, the C1’ – N glycosidic bond.

27
Q

Model of DNA as a Double Helix….

A

The specificity of base pairing permits duplication of genetic information - DNA replication.

Base pairs are always purine with a pyrimidine, so large with small, maintaining the helix
diameter… useful for
monitoring DNA integrity,
which is vital.

DNA can also base pair
with RNA: C-G & A-U,
antiparallel!

Biochemistry (14 decks)

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